diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt index 53e9949fb2..e440872661 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.denoising/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt index bca7bbf99c..159cd238a9 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.fiberfox/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt index 08da352f42..dcf135c587 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.fiberprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt index b46289df16..35b0da5e17 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.ivim/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt index cbedb4b8fe..654e260138 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.odfpeaks/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/CMakeLists.txt index 51ab328dbb..a5d753484d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.partialvolume/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/CMakeLists.txt index d566b94c3a..d944180266 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.preprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt index bcbe770470..341222ae5d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt @@ -1,10 +1,11 @@ # 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.python/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt index 2099cf1457..7ab1179c26 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt @@ -1,17 +1,18 @@ 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.reconstruction/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt index dd84875c28..5f0e2f510b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt @@ -1,9 +1,10 @@ # 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/QmitkTensorReconstructionViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkTensorReconstructionViewUserManual.dox index 42c24fc814..935571e18d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkTensorReconstructionViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkTensorReconstructionViewUserManual.dox @@ -1,18 +1,18 @@ /** \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. +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.registration/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt index ef0bf7b66f..a0dd6267f4 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.tbss/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt index ef61ef4be4..cda45e0351 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt @@ -1,9 +1,10 @@ # 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.tractography/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt index 8b52320a44..095d4e206a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt @@ -1,10 +1,11 @@ # 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/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt index ec856e5c14..7c8c92b85f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt @@ -1,7 +1,8 @@ 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.diffusionimagingapp/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimagingapp/CMakeLists.txt index 59fc92c1ec..80a74157e9 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/CMakeLists.txt @@ -1,8 +1,9 @@ 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 )