diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt
index 0a3bfaa0c2..7df47d093b 100644
--- a/Applications/Diffusion/CMakeLists.txt
+++ b/Applications/Diffusion/CMakeLists.txt
@@ -1,98 +1,76 @@
 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.common.legacy
-  org.mitk.gui.qt.datamanager
   org.mitk.gui.qt.measurementtoolbox
   org.mitk.gui.qt.segmentation
   org.mitk.gui.qt.volumevisualization
   org.mitk.gui.qt.diffusionimaging
-  org.mitk.gui.qt.diffusionimaging.connectomics
-  org.mitk.gui.qt.diffusionimaging.denoising
   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.partialvolume
   org.mitk.gui.qt.diffusionimaging.preprocessing
   org.mitk.gui.qt.diffusionimaging.reconstruction
-  org.mitk.gui.qt.diffusionimaging.registration
-  org.mitk.gui.qt.diffusionimaging.tbss
   org.mitk.gui.qt.diffusionimaging.tractography
+  org.mitk.gui.qt.diffusionimaging.connectomics
   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
-  org.mitk.gui.qt.cmdlinemodules
 )
 
 # 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/target_libraries.cmake b/Applications/Diffusion/target_libraries.cmake
index 8230101299..a6496917be 100644
--- a/Applications/Diffusion/target_libraries.cmake
+++ b/Applications/Diffusion/target_libraries.cmake
@@ -1,34 +1,29 @@
 
 # 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_common_legacy
   org_mitk_gui_qt_ext
   org_mitk_gui_qt_datamanager
   org_mitk_gui_qt_segmentation
   org_mitk_gui_qt_volumevisualization
   org_mitk_gui_qt_diffusionimaging
   org_mitk_gui_qt_diffusionimaging_connectomics
-  org_mitk_gui_qt_diffusionimaging_denoising
   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_partialvolume
   org_mitk_gui_qt_diffusionimaging_preprocessing
   org_mitk_gui_qt_diffusionimaging_reconstruction
-  org_mitk_gui_qt_diffusionimaging_registration
-  org_mitk_gui_qt_diffusionimaging_tbss
   org_mitk_gui_qt_diffusionimaging_tractography
   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
-  org_mitk_gui_qt_cmdlinemodules
 )
diff --git a/CMake/BuildConfigurations/DiffusionRelease.cmake b/CMake/BuildConfigurations/DiffusionRelease.cmake
index 47d66eb1f9..e356b9d707 100644
--- a/CMake/BuildConfigurations/DiffusionRelease.cmake
+++ b/CMake/BuildConfigurations/DiffusionRelease.cmake
@@ -1,78 +1,36 @@
 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)
 
 # 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_Fiberfox OFF CACHE BOOL "Build MITK Fiberfox" FORCE)
 set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE)
 
 # Activate Diffusion Mini Apps
 set(BUILD_DiffusionCoreCmdApps OFF 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 OFF CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE)
 set(BUILD_DiffusionQuantificationCmdApps OFF 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 OFF CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE)
 set(BUILD_DiffusionConnectomicsCmdApps ON 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(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
-
-# Activate required plugins
-# should be identical to the list in /Applications/Diffusion/CMakeLists.txt
-set(_plugins
-  org.commontk.configadmin
-  org.commontk.eventadmin
-  org.blueberry.compat
-  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.common.legacy
-  org.mitk.gui.qt.datamanager
-  org.mitk.gui.qt.measurementtoolbox
-  org.mitk.gui.qt.segmentation
-  org.mitk.gui.qt.volumevisualization
-  org.mitk.gui.qt.diffusionimaging
-  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.connectomics
-  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
-)