diff --git a/Modules/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp b/Modules/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp
index 534dcd7..38a5984 100644
--- a/Modules/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp
+++ b/Modules/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp
@@ -1,100 +1,88 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center.
 
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; 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 "mitkDiffusionCommandLineParser.h"
 #include <usAny.h>
 #include <mitkIOUtil.h>
 #include <mitkLexicalCast.h>
 #include <mitkCoreObjectFactory.h>
 #include <mitkPlanarFigure.h>
 #include <mitkPlanarFigureComposite.h>
 #include <mitkFiberBundle.h>
+#include <mitkDiffusionDataIOHelper.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[])
 {
   mitkDiffusionCommandLineParser 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", mitkDiffusionCommandLineParser::StringList, "Input:", "input tractograms", us::Any(), false);
   parser.addArgument("", "o", mitkDiffusionCommandLineParser::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;
 
   mitkDiffusionCommandLineParser::StringContainerType inFibs = us::any_cast<mitkDiffusionCommandLineParser::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); }
-    }
+    std::vector< mitk::FiberBundle::Pointer > tractograms = mitk::DiffusionDataIOHelper::load_fibs(inFibs);
+
+    mitk::FiberBundle::Pointer result = mitk::FiberBundle::New();
     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/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
index 008eef1..a2bd0f7 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
@@ -1,1825 +1,1825 @@
 <?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>
+    <width>953</width>
+    <height>1244</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>2</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>
+        <width>935</width>
+        <height>790</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 &quot;overlapping&quot;.</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="../../../../../release/MITK-build/private_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="../../../../../release/MITK-build/private_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>-48</y>
-        <width>353</width>
-        <height>456</height>
+        <y>0</y>
+        <width>907</width>
+        <height>850</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>Relative tract density (value between 0.0 and 1.0)</string>
             </property>
             <property name="decimals">
              <number>5</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>0.050000000000000</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>353</width>
-        <height>461</height>
+        <width>935</width>
+        <height>816</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="5" 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="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="4" column="0">
            <widget class="QComboBox" name="m_LookupTableTypeBox">
             <item>
              <property name="text">
               <string>JET</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>HOT_IRON</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>PLASMA</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>INFERNO</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>VIRIDIS</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>MAGMA</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>GRAYSCALE</string>
              </property>
             </item>
             <item>
              <property name="text">
               <string>MULTILABEL</string>
              </property>
             </item>
            </widget>
           </item>
           <item row="2" column="0">
            <widget class="QCheckBox" name="m_ValueAsWeightBox">
             <property name="toolTip">
              <string>If checked, the (mean) unnormalized values per fiber are also used as fiber weights, e.g. the fiber length in mm.</string>
             </property>
             <property name="text">
              <string>Values as weight</string>
             </property>
             <property name="checked">
              <bool>false</bool>
             </property>
            </widget>
           </item>
           <item row="3" column="0">
            <widget class="QFrame" name="frame_2">
             <property name="frameShape">
              <enum>QFrame::StyledPanel</enum>
             </property>
             <property name="frameShadow">
              <enum>QFrame::Raised</enum>
             </property>
             <property name="lineWidth">
              <number>0</number>
             </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="QLabel" name="label_17">
                <property name="text">
                 <string>Value cap:</string>
                </property>
               </widget>
              </item>
              <item row="0" column="1">
               <widget class="QDoubleSpinBox" name="m_PercentileBox">
                <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>0.950000000000000</double>
                </property>
               </widget>
              </item>
             </layout>
            </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>Mirror fibers</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Weight bundle</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color fibers by fiber weights</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color &amp; weight fibers by curvature</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color &amp; weight fibers by length</string>
           </property>
          </item>
          <item>
           <property name="text">
            <string>Color &amp; weight fibers by scalar map (e.g. FA)</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>
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  <connections/>
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diff --git a/README.md b/README.md
index 84d22e9..6960dd2 100644
--- a/README.md
+++ b/README.md
@@ -1,255 +1,255 @@
 MITK Diffusion
 ==============
 
 Copyright © German Cancer Research Center (DKFZ), [Division of Medical Image Computing (MIC)](https://www.dkfz.de/en/mic/index.php). Please make sure that your usage of this code is in compliance with the code [license](https://github.com/MIC-DKFZ/MITK-Diffusion/blob/master/LICENSE.txt).
 
 [![DOI](https://zenodo.org/badge/195387051.svg)](https://zenodo.org/badge/latestdoi/195387051)
 
 The MITK Diffusion application [[1,2]](#References) offers a selection of image analysis algorithms for the processing of diffusion-weighted MR images. It encompasses the research of the Division of Medical Image Computing at the German Cancer Research Center (DKFZ).
 
 * [Downloads](#Downloads)
 * [Requirements](#Requirements)
 * [Features](#Features)
 * [Related Links](#Related-Links)
 * [Image Gallery](#Image-Gallery)
 * [Building MITK Diffusion from source](#Building-MITK-Diffusion-from-source)
 * [User Manual](http://docs.mitk.org/diffusion/nightly/)
 * [Report a Bug](https://phabricator.mitk.org/maniphest/task/edit/form/29/)
 * [References](#References)
 * [Contact](#Contact)
 
 ## Downloads
 
 Please have a look at the [requirements](#Requirements) for running MITK Diffusion with all its features successfully!
 
 The nightly builds come as executable setup wizards that install MITK Diffusion on your system or alternatively as simple .tar.gz or .zip archive where you can execute MITK Diffusion and the command line apps "manually". Should there be no new installer for a while, please [contact](#Contact) us and report the issue.
 
 **Without Python Support (standard)**:
 * [Ubuntu 20.04 executable installer](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_ubuntu-20.04_NoPython.run.html)
 * [Ubuntu 20.04 tarball archive](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_ubuntu-20.04_NoPython.tar.gz.html)
 * [Windows 10 executable installer](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_Windows-10_NoPython.exe.html)
 * [Windows 10 zip archive](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_Windows-10_NoPython.zip.html)
 
 **With Python Support (experimental)**:
 * [Ubuntu 20.04 executable installer](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_ubuntu-20.04_Python.run.html)
 * [Ubuntu 20.04 tarball archive](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_ubuntu-20.04_Python.tar.gz.html)
 * [Windows 10 executable installer](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_Windows-10_Python.exe.html)
 * [Windows 10 zip archive](http://www.mitk.org/download/diffusion/nightly/MITK-Diffusion_Windows-10_Python.zip.html)
 
 
 If you encounter any bugs, please report them in our [bugtracking](https://phabricator.mitk.org/maniphest/task/edit/form/29/) system or use the [MITK-users mailing list](http://mitk.org/wiki/MITK_Mailinglist). We are grateful for any feedback!
 
 
 ### Requirements
 
 * Install Python 3.X: `sudo apt install python3 python3-pip` (Ubuntu) or from https://www.python.org/downloads/windows/ (Windows)
 * Download our Python requirements file: [PythonRequirements.txt](https://github.com/MIC-DKFZ/MITK-Diffusion/tree/master/PythonRequirements.txt)
 * Install the Python requirements: `pip3 install -r PythonRequirements.txt`
 * If your are behind a proxy use `pip3 --proxy <proxy> install -r PythonRequirements.txt`
 
 **For Windows users**:
 MITK Diffusion requires the Microsoft Visual C++ 2017 Redistributable to be installed on the system. The MITK Diffusion installer automatically installs this redistributable for you if not already present on the system, but it needs administrative privileges to do so. So to install the redistributable, **run the MITK Diffusion installer as administrator**.
 
 ## Features
 
 **Support for most established image formats**
 * Images: DICOM, NIFTI, NRRD (peak and SH images compatible with MRtrix)
 * Tractograms: fib/vtk, tck and trk.
 
 **Image preprocessing**
 * Registration
 * Head-motion correction
 * Denoising
 * Skull stripping and brain mask segmentation (Linux only)
 * Resampling, cropping, flipping and merging
 * Header modifications
 * Single volume extraction
 
 **Diffusion gradient/b-value processing**
 * b-value rounding
 * Gradient direction flipping
 * Gradient direction subsampling
 * Averaging of gradient directions/volumes
 * Gradient direction and b-value visualization
 
 **ODF reconstruction and signal modelling**
 * Tensor and Q-ball reconstruction
 * Other reconstructions via Dipy wrapping (CSD, 3D SHORE, SFM) (Linux only)
 * ODF peak calculation
 * MRtrix or camino results can be imported
 
 **Quantification of diffusion-weighted/tensor/ODF images**
 * Intravoxel Incoherent Motion (IVIM) and diffusion kurtosis analysis
 * Calculation of many other derived indices such as ADC, MD, GFA, FA, RA, AD, RD
 * Image statistics
 
 **Segmentation**
 * Automatic white matter bundle segmentation (TractSeg) [[3]](#References) (Linux only)
 * Automatic brain mask segmentation (Linux only)
 * Manual image segmentation and operations on segmentations
 * SOON: automatic brain tissue segmentation
 
 **Fiber tractography**
 * Global tractography [[4]](#References)
 * Streamline tractography
     * Interactive (similar to [[5]](#References)) or seed image based
     * Deterministic or probabilistic
     * Peak, ODF, tensor and raw dMRI based. The latter one in conjunction with machine learning based tractography [[6]](#References)
     * Various possibilities for anatomical constraints.
     * Tractography priors in form of additional peak images, e.g. obtained using TractSeg
 
 **Fiber processing**
 * Tract dissection (parcellation or ROI based)
 * Tract filtering by
     * length
     * curvature
     * direction
     * weight
     * density
 * Tract resampling and compression
 * Tract transformation
     * Mirroring
     * Rotating and translating
     * Registration (apply transform of previously performed image registration)
 * Tract coloring
     * Curvature
     * Length
     * Weight
     * Scalar map (e.g. FA)
 * Other operations
     * Join
     * Subtract
     * Copy
 * Fiber clustering [[7]](#References)
 * Fiber fitting and weighting similar to SIFT2 and LiFE [[8,9]](#References)
 * Principal direction extraction (fibers --> peaks)
 * Tract derived images:
     * Tract density images
     * Tract endpoint images
     * Tract envelopes
 
 **Fiberfox dMRI simulations** [[10]](#References)
 * Multi-compartment signal modeling
 * Simulation of the k-space acquisition including
     * Compartment specific relaxation effects
     * Artifacts such as noise, spikes, ghosts, aliasing, distortions, signal drift, head motion, eddy currents and Gibbs ringing
     * Definition of important acquisition parameters such as bvalues and gradient directions, TE, TR, dwell time, partial Fourier, ...
 * Manual definition of fiber configurations, e.g. for evaluation purposes
 * Automatic generation of random fiber configurations
 
 **Other features**
 * Brain network statistics and visualization (connectomics)
 * Interactive Python console (Linux only)
 * Integrated screenshot maker
 * Command line tools for most functionalities
 
 ## Related Links
-* Great python package for logging your (MITK) command line experiments:
+* Great python package for logging your (MITK or other) command line experiments:
     * https://github.com/MIC-DKFZ/cmdint
     * `pip3 install cmdint`
 * TractSeg reference data of 72 semiautomatically defined bundles in 105 HCP subjects: https://zenodo.org/record/1285152
 * TractSeg python package: https://github.com/MIC-DKFZ/TractSeg
 * Simulated dMRI images and ground truth of random fiber phantoms in various configurations: https://doi.org/10.5281/zenodo.2533250
 * ISMRM 2015 Tractography Challenge Data: https://doi.org/10.5281/zenodo.572345 & https://doi.org/10.5281/zenodo.1007149
 
 
 ## Image Gallery
 
 ![](http://mitk.org/images/8/8f/MitkDiffusion.png) Screenshot of the MITK Diffusion Welcome Screen
 <br/><br/><br/>
 
 ![](http://mitk.org/images/0/09/ScalarMaps.png) Scalar map visualization
 <br/><br/><br/>
 
 ![](http://mitk.org/images/3/3b/Data_Tensors.png) Tensor Visualization
 <br/><br/><br/>
 
 ![](http://mitk.org/images/5/5c/Data_ODF.png) ODF visualization
 <br/><br/><br/>
 
 ![](http://mitk.org/images/7/73/Data_Peaks.png) Peak visualization (uniform white coloring)
 <br/><br/><br/>
 
 ![](http://mitk.org/images/6/68/StreamlineTractography.png) Interactive tractography in MITK Diffusion. The tractogram updates automatically on parameter change and movement of the spherical seed region.
 <br/><br/><br/>
 
 ![](http://mitk.org/images/3/3a/Extraction_1.png) Tract dissection using manually drawn ROIs.
 <br/><br/><br/>
 
 ![](http://mitk.org/images/f/f5/FiberFit.png) Automatic streamline weighting (similar to SIFT2 or LiFE)
 <br/><br/><br/>
 
 ![](http://mitk.org/images/3/33/Fiberfox.png) Illustration of the dMRI phantom simulation process using Fiberfox.
 <br/><br/><br/>
 
 <img src="http://mitk.org/images/e/ec/Eddy.gif" width="250" height="200" /><img src="http://mitk.org/images/a/ad/Spike_and_motion.gif" width="250" height="200" /><img src="http://mitk.org/images/8/8e/Drift.gif" width="250" height="200" />
 <img src="http://mitk.org/images/0/08/645551_axial_motion_ghost_eddy.gif" width="250" height="200" /><img src="http://mitk.org/images/5/55/Ringing.gif" width="250" height="200" /><img src="http://mitk.org/images/3/37/683256_Distortions_Sagittal.gif" width="250" height="200" />\
 Illustration of simulated dMRI images with various artifacts (a bit excessive for illustration purposes): eddy current distortions (1), motion and spike (2), intensity drift (3), motion, eddy and noise (4), ringing (5), B0 inhomogeneity distortions (6), from left to right.
 <br/><br/><br/>
 
 ![](http://mitk.org/images/0/08/RandomFibers_Example.png)
 Automatically generated random fiber configuration for Fiberfox simulations.
 <br/><br/><br/>
 
 
 ## Building MITK Diffusion from source
-* Install [Qt](https://www.qt.io/) on your system (>= 5.12.6).
+* Install [Qt](https://www.qt.io/) on your system (5.12).
 * Clone MITK from [github](https://github.com/MIC-DKFZ/MITK-Diffusion.git) using [Git version control](https://git-scm.com/).
 * Clone MITK Diffusion from [github](https://github.com/MITK/MITK.git).
-* Configure the MITK Superbuild using [CMake](https://cmake.org/) (>= 3.14.5).
+* Configure the MITK Superbuild using [CMake](https://cmake.org/) (>= 3.18).
     * Choose the MITK source code directory and an empty binary directory.
     * Click "Configure".
     * Set the option MITK_EXTENSION_DIRS to "/path/to/my/mitk-diffusion-repository".
     * Click "Configure".
     * Set the option MITK_BUILD_CONFIGURATION to "DiffusionRelease".
     * Click "Generate".
     * macOS specifics (unclear if this still applies):
         * Use python 3.**6**, since python 3.**7** leads to build errors on macOS.
         * The cmake variables for python 3 might need to be set manually. It is probably enough to specify PYTHON_EXECUTABLE.
         * Openmp needs to be installed manually since it is not included in apple clang anymore: "brew install libomp" should do the trick. It might be necessary to set the corresponding make variables later in the MITK build manually:
             * OpenMP_CXX_FLAGS: -Xpreprocessor -fopenmp -I"/path/to/python3/includes/"
             * OpenMP_C_FLAGS: -Xpreprocessor -fopenmp -I"/path/to/python3/includes/"
             * OpenMPCXX_LIB_NAMES: libomp
             * OpenMPC_LIB_NAMES: libomp
             * OpenMP_libomp_LIBRARY: /path/to/libomp.dylib
 * Start the Superbuild:
     * Linux/maxOS: Open a console window, navigate to the build folder and type "make -j8" (optionally supply the number threads to be used for a parallel build with -j).
     * Windows (requires visual studio): Open the MITK Superbuild solution file and build all projects.
     * The Superbuild may take some time.
     * After the Superbuild has finished, change the cmake binary directory from "/path/to/my/build" to "/path/to/my/build/MITK-build" and configure+generate again.
     * Build again in "/path/to/my/build/MITK-build" using make (linux/mac) or the VS solution file.
     * The build may again take some time and should yield the binaries in "/path/to/my/build/MITK-build/bin"
 
 More detailed build instructions can be found in the [documentation](http://docs.mitk.org/nightly/BuildInstructionsPage.html).
 
 
 Continuous integration: https://cdash.mitk.org/index.php?project=MITK-Diffusion
 
 
 ## References
 
 All publications of the Division of Medical Image Computing can be found [https://www.dkfz.de/en/mic/publications/ here].
 
 [1] Fritzsche, Klaus H., Peter F. Neher, Ignaz Reicht, Thomas van Bruggen, Caspar Goch, Marco Reisert, Marco Nolden, et al. “MITK Diffusion Imaging.” Methods of Information in Medicine 51, no. 5 (2012): 441.
 
 [2] Fritzsche, K., and H.-P. Meinzer. “MITK-DI A New Diffusion Imaging Component for MITK.” In Bildverarbeitung Für Die Medizin, n.d.
 
 [3] Wasserthal, Jakob, Peter Neher, and Klaus H. Maier-Hein. “TractSeg - Fast and Accurate White Matter Tract Segmentation.” NeuroImage 183 (August 4, 2018): 239–53.
 
 [4] Neher, P. F., B. Stieltjes, M. Reisert, I. Reicht, H.P. Meinzer, and K. Maier-Hein. “MITK Global Tractography.” In SPIE Medical Imaging: Image Processing, 2012.
 
 [5] Chamberland, M., K. Whittingstall, D. Fortin, D. Mathieu, und M. Descoteaux. „Real-time multi-peak tractography for instantaneous connectivity display“. Front Neuroinform 8 (2014): 59. doi:10.3389/fninf.2014.00059.
 
 [6] 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.
 
 [7] 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).
 
 [8] 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.
 
 [9] 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.
 
 [10] Neher, Peter F., Frederik B. Laun, Bram Stieltjes, and Klaus H. Maier-Hein. “Fiberfox: Facilitating the Creation of Realistic White Matter Software Phantoms.” Magnetic Resonance in Medicine 72, no. 5 (November 2014): 1460–70. doi:10.1002/mrm.25045.
 
 
 ## Contact
 If you have questions about the application or if you would like to give us feedback, don't hesitate to contact us using [our mailing list](http://mitk.org/wiki/MITK_Mailinglist) or, for questions that are of no interest for the community, [directly](https://www.dkfz.de/en/mic/team/people/Peter_Neher.html).