diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 67ac20c7c5..ad3769bb0b 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,68 +1,77 @@ /** \page PluginListPage MITK Plugin Manuals \section PluginListPageOverview Overview The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed. The distinction between developer and end user use is for convenience only and mainly distinguishes which group a plugin is primarily aimed at. \section PluginListPageEndUserPluginList List of Plugins for End User Use \li \subpage org_blueberry_ui_qt_log \li \subpage org_mitk_views_basicimageprocessing \li \subpage org_mitk_views_cmdlinemodules \li \subpage org_mitk_views_datamanager \li \subpage org_mitk_gui_qt_dicom \li \subpage org_mitk_gui_qt_dicominspector \li \subpage org_mitk_gui_qt_diffusionimaging \li \subpage org_mitk_gui_qt_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_gui_qt_moviemaker \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_python \li \subpage org_mitk_gui_qt_remeshing \li \subpage org_mitk_views_segmentation \li \subpage org_mitk_views_multilabelsegmentation \li \subpage org_mitk_gui_qt_spectrocamrecorder \li \subpage org_mitk_gui_qt_ultrasound \li \subpage org_mitk_gui_qt_viewnavigator \li \subpage org_mitk_views_volumevisualization \li \subpage org_mitk_gui_qt_xnat \li \subpage org_mitk_gui_qt_aicpregistration \li \subpage org_mitk_gui_qt_igtlplugin \li \subpage org_mitk_gui_qt_geometrytools \li \subpage org_mitk_gui_qt_classificationsegmentation \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control \li \subpage org_mitk_gui_qt_matchpoint_evaluator \li \subpage org_mitk_gui_qt_matchpoint_framereg \li \subpage org_mitk_gui_qt_matchpoint_manipulator \li \subpage org_mitk_gui_qt_matchpoint_mapper \li \subpage org_mitk_gui_qt_matchpoint_visualizer \li \subpage org_mitk_gui_qt_cest + \li \subpage org_mitk_gui_qt_fit_genericfitting + \li \subpage org_mitk_gui_qt_fit_inspector + \li \subpage org_mitk_gui_qt_pharmacokinetics_mri + \li \subpage org_mitk_gui_qt_pharmacokinetics_pet + \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri + \li \subpage org_mitk_gui_qt_pharmacokinetics_curvedescriptor \section PluginListPageDevPluginList List of Plugins for Developer Use and Examples \li \subpage org_surfacematerialeditor \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_examples \li \subpage org_mitkexamplesopencv \li \subpage org_mitk_gui_qt_igtexample \li \subpage org_mitk_gui_qt_igttracking \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_blueberry_ui_qt_objectinspector \li \subpage org_mitk_gui_qt_eventrecorder \li \subpage org_mitk_gui_qt_overlaymanager \li \subpage org_mitk_example_gui_pcaexample \li \subpage org_mitk_gui_qt_renderwindowmanager \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement + \li \subpage org_mitk_gui_qt_fit_demo + \li \subpage org_mitk_gui_qt_pharmacokinetics_simulation + */ diff --git a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox index e6ce7d7afa..17a7551190 100644 --- a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/Manual.dox @@ -1,9 +1,17 @@ /** -\page org_mitk_gui_qt_fit_demo The Fit Demo View +\page org_mitk_gui_qt_fit_demo The Model Fit Demo View -\li \ref FDEMO_Introduction +\imageMacro{fit_demo_doc.svg,"Icon of the Fit Demo View",3.0} + +\tableofcontents + +\section FIT_DEMO_Introduction Introduction +This plugin is a very simple demo plugin that allows 1) to generate a demo 3D+t image (with linear increasing values) and 2) to perform a linear fit on a selected node. +It was/is use to demonstrate basic principle and to generate example fit sessions for demo and testing purposes (e.g. functionality of the fit inspector). + +\section FIT_DEMO_Contact Contact information +This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). If you have any questions, need support, +find a bug or have a feature request, feel free to contact us at www.mitk.org. -\section FDEMO_Introduction Introduction -This is a very simple view that demonstrates how a fit generator can be implemented using the module ModelFit. -In addition the view can be used to generate a demo fit to explore other components like the fit explorer. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/fit_demo_doc.svg b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/fit_demo_doc.svg new file mode 100644 index 0000000000..d8be4ff405 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.demo/documentation/UserManual/fit_demo_doc.svg @@ -0,0 +1,177 @@ + + + +image/svg+xml + + +FIT + + + + +DEMO + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.demo/files.cmake b/Plugins/org.mitk.gui.qt.fit.demo/files.cmake index 978d11fb67..d58f4a7b32 100644 --- a/Plugins/org.mitk.gui.qt.fit.demo/files.cmake +++ b/Plugins/org.mitk.gui.qt.fit.demo/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_FitGeneratorDemo_Activator.cpp FitGeneratorDemoView.cpp ) set(UI_FILES src/internal/FitGeneratorDemoView.ui ) set(MOC_H_FILES src/internal/org_mitk_FitGeneratorDemo_Activator.h src/internal/FitGeneratorDemoView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/demo.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml b/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml index 671cc92071..1ac84c636b 100644 --- a/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml +++ b/Plugins/org.mitk.gui.qt.fit.demo/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.fit.demo/resources/demo.png b/Plugins/org.mitk.gui.qt.fit.demo/resources/demo.png deleted file mode 100644 index 245959d54e..0000000000 Binary files a/Plugins/org.mitk.gui.qt.fit.demo/resources/demo.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.fit.demo/resources/icon.svg b/Plugins/org.mitk.gui.qt.fit.demo/resources/icon.svg new file mode 100644 index 0000000000..9227dbceb3 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.demo/resources/icon.svg @@ -0,0 +1,172 @@ + + + +image/svg+xml + + +FIT + + + +DEMO + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox index f4022f946f..22989ba6dd 100644 --- a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox @@ -1,8 +1,16 @@ /** -\page org_mitk_gui_qt_fit_genericfitting The Generic Fitting View +\page org_mitk_gui_qt_fit_genericfitting The Model Fit Generic Fitting View -\section org_mitk_gui_qt_fit_genericfitting_Overview Overview +\imageMacro{fit_generic_doc.svg,"Icon of the Generic Fitting View",3.0} + +\tableofcontents + +\section FIT_GENERIC_Introduction Introduction This plug-in offers a generic fitting component for time resolved image data. +\section FIT_GENERIC_Contact Contact information +This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). If you have any questions, need support, +find a bug or have a feature request, feel free to contact us at www.mitk.org. -*/ +*/ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/fit_generic_doc.svg b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/fit_generic_doc.svg new file mode 100644 index 0000000000..3e4cab1381 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/fit_generic_doc.svg @@ -0,0 +1,181 @@ + + + +image/svg+xml + + +FIT + + + + + + + + + + + + +DATA + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/files.cmake b/Plugins/org.mitk.gui.qt.fit.genericfitting/files.cmake index 177d57ce0e..f4f3d533f5 100644 --- a/Plugins/org.mitk.gui.qt.fit.genericfitting/files.cmake +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_GenericDataFittingView_Activator.cpp GenericDataFittingView.cpp ) set(UI_FILES src/internal/GenericDataFittingViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_GenericDataFittingView_Activator.h src/internal/GenericDataFittingView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/gdf.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/plugin.xml b/Plugins/org.mitk.gui.qt.fit.genericfitting/plugin.xml index 5ab18734b8..c77936d932 100644 --- a/Plugins/org.mitk.gui.qt.fit.genericfitting/plugin.xml +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/resources/gdf.png b/Plugins/org.mitk.gui.qt.fit.genericfitting/resources/gdf.png deleted file mode 100644 index c6c3dd3d93..0000000000 Binary files a/Plugins/org.mitk.gui.qt.fit.genericfitting/resources/gdf.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/resources/icon.svg b/Plugins/org.mitk.gui.qt.fit.genericfitting/resources/icon.svg new file mode 100644 index 0000000000..74de187fd7 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/resources/icon.svg @@ -0,0 +1,180 @@ + + + +image/svg+xml + + +FIT + + + + + + + + + + + + + + +DATA + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png new file mode 100644 index 0000000000..6caf5dafe0 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox index e8e7fcb587..edd1f3e8a5 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox @@ -1,14 +1,78 @@ /** -\page org_mitk_gui_qt_fit_inspector Model Fit Inspector +\page org_mitk_gui_qt_fit_inspector The Model Fit Inspector View -\image html mf.png "Icon of Model Fit Inspector" +\imageMacro{fit_inspector_doc.svg,"Icon of the Model Fit Inspector View",3.0} -Available sections: - - \ref org_mitk_gui_qt_fit_inspectorOverview +\tableofcontents -\section org_mitk_gui_qt_fit_inspectorOverview Overview -The view can be used to inspect the following things: -#1 raw data if it has multiple time steps -#2 Fits and the fitted data +\section FIT_INSPECTOR_Introduction Introduction +This view (Model Fit Inspector; MFI) offers the possibility to display the time course of the signal within an individual +voxel (with or without fit). +\section FIT_INSPECTOR_Contact Contact information +This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). If you have any questions, need support, +find a bug or have a feature request, feel free to contact us at www.mitk.org. + +\section FIT_INSPECTOR_Raw Viewing without a model fit +\imageMacro{fit_inspect_raw.png, "Example screen shot showing the inspection of raw dynamic data without a fit.", 10} +Open the view and select the dynamic image in the data manager. +The graph plot will show the time course of image intensities (signal) in the selected voxel (cross hair) as red data points. +The blue point indicates the frame currently displayed in the 4-window view. + +\section FIT_INSPECTOR_Fit Viewing without a model fit +\imageMacro{fit_inspect_fit.png, "Example screen shot showing the inspection of dynamic data and an associated fit.", 10} +Selecting a parameter map of the fit of interest in the Data Manager will display the raw data curve in red dots with +corresponding fit as black line in the selected cross-hair position. If an AIF-based model was used, +the utilized AIF (averaged over AIF mask) is also displayed (default in green). The color of the AIF display can be adjusted. +For ROI based fits, the MFI will display both the current data curve in the selected voxel (in red) +and the ROI-averaged fitted curve (in dark green, can be adjusted). Scrolling through the individual voxels will change +the current data curve, but the ROI-based curve remains the same. If voxels outside the fitted area defined by the mask +are selected, the raw data voxel values will be displayed, however no black fit line is visualized. + +Below the data plot, several options for data visualization can be selected: +\subsection FIT_INSPECTOR_Fit_info Fit info tab +\imageMacro{fit_inspect_info.png, "Details of the fit info tab.", 5} +The Fit info tab displays meta-data for selected fits performed on the displayed data set. If no fit was performed and only raw data is visualized, the fields are empty. + +\subsection FIT_INSPECTOR_Fit_Parameter Fit parameter tab +\imageMacro{fit_inspect_results.png, "Details of the fit parameter tab.", 5} +The "fit parameter" tab shows fit related parameter estimate values, derived parameters, fit criterion values and (optional) debug parameter maps +in the selected voxel (and all inspection positions; see also \ref FIT_INSPECTOR_Inspect "inspection positions") listed as a table. +If no fit was performed and only raw data is visualized, the table is empty. +The content of the table may by copied to clipboard or exported as csv file, by clicking the respective button below the table. + +\subsection FIT_INSPECTOR_Fit_Inspection Inspection positions tab +\imageMacro{fit_inspect_positions.png, "Details of the inspection position tab.", 5} +The tab allows to manage inspection positions (see here for more about \ref FIT_INSPECTOR_Inspect "inspection positions"). +- (1) Shows the coordinates of the current selected position in the workbench. +- (2) Press to make the current position a inspected position. It will be added at the bottom of the list (3). +- (3) List of all inspection positions +- (4) Toggle adding mode on/off. If on, you can add new positions by clicking into render windows with "SHIFT + left mouse button". +- (5) Manually adding inspection positions by entering the coordinates. +- (6) Remove the selected inspection positions. (Hot key: Del) +- (7) Move the selected inspection position up in the list (3). +- (8) Move the selected inspection position down in the list (3). +- (9) Save inspection points to a file. +- (10) Load inspection points from a file. + +\subsection FIT_INSPECTOR_Fit_Settings Settings tab +\imageMacro{fit_inspect_settings.png, "Details of the settings tab.", 5} +The View settings tab is used to adjust the plot display, namely, x and y axis scales and colors of displayed data plots (i.e. AIF). + +\subsection FIT_INSPECTOR_Fit_Export Plot data export tab +\imageMacro{fit_inspect_export.png, "Details of the plot data export tab.", 5} +Displays voxel data (input image) and corresponding time grid together with model fit values and additional curves (like AIF values) for each time point. +The table will contain the position depended values of the current selected position as well as of all inspection positions (see also \ref FIT_INSPECTOR_Inspect "inspection positions"). +The data in the table can also be copied to clipboard or exported to csv files, by clicking the respective button below the table. + +\section FIT_INSPECTOR_Inspect Inspection positions +\imageMacro{fit_inspect_positions_example.png, "Example of the usage of inspection positions.", 5} +The fit inspector allows to define positions in the world coordinate system that will be constantly displayed in addition to the current selected position. +These inspected position will be shown in the following parts of the view: +- The plot windows. See example image above; the plot shows the current position (raw data: red dots, fit: black line) and an additional inspection position (green). +- The fit parameter tab (see example image above) +- The plot data export tab. + +It will work with dynamic data with and without an model fit. See the \ref FIT_INSPECTOR_Fit_Inspection "inspection positions tab section" for more details on how to manage inspection positions. */ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png new file mode 100644 index 0000000000..c6e28b8504 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png new file mode 100644 index 0000000000..39135d7a61 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png new file mode 100644 index 0000000000..db85415509 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png new file mode 100644 index 0000000000..6d5c46c456 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.svg b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.svg new file mode 100644 index 0000000000..2c06338905 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.svg @@ -0,0 +1,501 @@ + + + + + + + + + + image/svg+xml + + + + + + + + + + 1 + + + + + 2 + + + + + 3 + + + + + 4 + + + + + 5 + + + + + 6 + + + + + 7 + + + + + 8 + + + + + 9 + + + + + 10 + + + + diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png new file mode 100644 index 0000000000..ddfef4b2c1 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png new file mode 100644 index 0000000000..c333213f75 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png new file mode 100644 index 0000000000..49a74507ce Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png new file mode 100644 index 0000000000..ffedbddbfe Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspector_doc.svg b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspector_doc.svg new file mode 100644 index 0000000000..02b0cccaa1 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspector_doc.svg @@ -0,0 +1,156 @@ + + + +image/svg+xml + + +FIT + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/mf.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/mf.png deleted file mode 100644 index 68c73e7bba..0000000000 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/mf.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/files.cmake b/Plugins/org.mitk.gui.qt.fit.inspector/files.cmake index 8c449f52ae..b6b8dbca66 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/files.cmake +++ b/Plugins/org.mitk.gui.qt.fit.inspector/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_fit_inspector_Activator.cpp ModelFitInspectorView.cpp ) set(UI_FILES src/internal/ModelFitInspectorViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_fit_inspector_Activator.h src/internal/ModelFitInspectorView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/mf.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES resources/ModelFitInspector.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml b/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml index 10c679659b..3a24f2ddb5 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml +++ b/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/resources/icon.svg b/Plugins/org.mitk.gui.qt.fit.inspector/resources/icon.svg new file mode 100644 index 0000000000..ad5b8d6f58 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.fit.inspector/resources/icon.svg @@ -0,0 +1,150 @@ + + + +image/svg+xml + + +FIT + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/resources/mf.png b/Plugins/org.mitk.gui.qt.fit.inspector/resources/mf.png deleted file mode 100644 index d5e1d3d4fe..0000000000 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/resources/mf.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox index 8bb4491add..97e5f59a25 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox @@ -1,10 +1,16 @@ /** \page org_mitk_gui_qt_pharmacokinetics_concentration_mri The Concentration Curve Converter View -\li \ref org_mitk_gui_qt_pharmacokinetics_concentration_mri_Introduction +\imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the Concentration Curve Converter View",3.0} -\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_Introduction Introduction -This view offers the to posibility to convert MRI image signals into concentration images. -Theses concentration images can e.g. be used for perfusion model fitting. +\tableofcontents + +\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_overview Overview +Stand-alone conversion of image signal intensities to contrast agent concentration units can be performed with a dedicated plugin. The plugin distinguishes between T1 weighted and T2 weighted sequences. T1 conversion can be performed in terms of absolute and relative signal enhancement as well as turbo flash sequences for both 3D images (baseline images S0 without contrast enhancement (pre-contrast) input required) and 4D sequences (baseline selected as first frame of time series). + +\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_Contact Contact information +This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). +If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/pharmacokinetics_concentration_doc.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/pharmacokinetics_concentration_doc.svg new file mode 100644 index 0000000000..f31fed25f2 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/pharmacokinetics_concentration_doc.svg @@ -0,0 +1,153 @@ + + + +image/svg+xml + + +DCE + + + + + + +CONC + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/files.cmake b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/files.cmake index 17c9dffd99..71983f82d6 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/files.cmake +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_ConcentrationCurveConverterView_Activator.cpp ConcentrationCurveConverterView.cpp ) set(UI_FILES src/internal/ConcentrationCurveConverterViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_ConcentrationCurveConverterView_Activator.h src/internal/ConcentrationCurveConverterView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/Convert.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml index fead26d528..ca8c8a0fe5 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/resources/Convert.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/resources/Convert.png deleted file mode 100644 index 5c18097572..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/resources/Convert.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/resources/icon.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/resources/icon.svg new file mode 100644 index 0000000000..ddc396ee8f --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/resources/icon.svg @@ -0,0 +1,152 @@ + + + +image/svg+xml + + +DCE + + + + + + +CONC + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox index 494b785680..b1e55f62a7 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/Manual.dox @@ -1,4 +1,26 @@ /** \page org_mitk_gui_qt_pharmacokinetics_curvedescriptor The Perfusion Curve Description Parameters View +\imageMacro{pharmacokinetics_curve_desc_doc.svg,"Icon of the Perfusion Curve Description Parameters View",3.0} + +\tableofcontents + +\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_overview Overview +In cases where data quality is not sufficient for dedicated pharmacokinetic analysis, or if global scouting of the overall image should be performed to identify regions of interest, it is often advisable to use semi-quantitative measures that describe the general shape and type of the curve. The Perfusion Curve Description Parameters plugin can be used to voxelwise calculate these parameters. +Currently the following parameters are offered by the tool: +- area-under-the-curve (AUC) +- area-under the first moment curve (AUMC), +- mean-residence-time (MRT; AUMC/AUC) +- time to peak and maximum signal + +These parameters are calculated directly from the sampled data. +AUC and AUMC are calculated by step-wise integration with linear interpolation between sampling points. Maximum and time to peak are derived from the highest intensity value (overall maximum) of all data points. +Note: If semi-quantitative parameters should be calculated from concentration time curves rather than raw data signal intensities, use the concentration n curve converter view (See 5) +Parameters of interest can be selected from the list. Selecting a 4D image in the Data manager enables the Calculate Parameters button. Resulting parameter maps will afterwards be added to the data manager as subnodes to the analyzed 4D image. + +\section org_mitk_gui_qt_pharmacokinetics_concentration_mri_Contact Contact information +This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). +If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. + */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/pharmacokinetics_curve_desc_doc.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/pharmacokinetics_curve_desc_doc.svg new file mode 100644 index 0000000000..5647369b71 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/documentation/UserManual/pharmacokinetics_curve_desc_doc.svg @@ -0,0 +1,252 @@ + + + +image/svg+xml + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/files.cmake b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/files.cmake index 4d3cf1bb68..b68e376416 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/files.cmake +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_PerfusionCurveDescriptionParameterView_Activator.cpp PerfusionCurveDescriptionParameterView.cpp ) set(UI_FILES src/internal/PerfusionCurveDescriptionParameterViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_PerfusionCurveDescriptionParameterView_Activator.h src/internal/PerfusionCurveDescriptionParameterView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/icon.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml index 42dadcd43e..3239639a5f 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon.png deleted file mode 100644 index 08673d42f2..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon.svg new file mode 100644 index 0000000000..acf4338cef --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon.svg @@ -0,0 +1,236 @@ + + + +image/svg+xml + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon_PerfusionCurveDescriptors.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon_PerfusionCurveDescriptors.png deleted file mode 100644 index fb87d9e608..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon_PerfusionCurveDescriptors.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon_raw.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon_raw.svg new file mode 100644 index 0000000000..f09d986910 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/icon_raw.svg @@ -0,0 +1,233 @@ + + + +image/svg+xml + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/petsuv.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/petsuv.png deleted file mode 100644 index 2dc586dfd4..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/resources/petsuv.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox index b5529a4a2e..ab56d736e1 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox @@ -1,8 +1,88 @@ /** \page org_mitk_gui_qt_pharmacokinetics_mri The DCE MR Perfusion Datafit View -\section org_mitk_gui_qt_pharmacokinetics_mri_Overview Overview +\imageMacro{pharmacokinetics_mri_doc.svg,"Icon of the DCE MR Perfusion View",3.0} + +\tableofcontents + +\section FIT_DCE_Introduction Introduction +For pharmacokinetic analysis of DCE MRI/CT data using compartment models in non-linear least square fitting the DCE MR Perfusion Datafit plugin can be used. + +\section FIT_DCE_Contact Contact information +This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). +If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. +\subsection FIT_DCE_Cite Citation information +If you use the view for your research please cite our work as reference:\n\n +Debus C and Floca R, Ingrisch M, Kompan I, Maier-Hein K, Abdollahi A, Nolden M, MITK-ModelFit: generic open-source framework for model fits and their exploration in medical imaging – design, implementation and application on the example of DCE-MRI (arXiv:1807.07353) + +\section FIT_DCE_General General information +\imageMacro{dce_mri_init.png, "Example screen shot showing the view at first start.", 10} +For pharmacokinetic analysis of DCE MRI/CT data using compartment models in non-linear least square fitting the DCE MR Perfusion Datafit view can be used. +In principle, every model can be fitted on the entire image. However, for model configuration reasons (e.g. AIF required) and computational time cost, this is often not advisable. +Therefore, apart from the image to be fitted (Selected Time Series), a ROI segmentation can be defined (Selected Mask), within which model fitting is performed. +The view currently offers voxel wise and/or ROI averaged fits of intensity-time curves with different quantitative and semi-quantitative models. +If a mask is selected, ROI-based fitting (fit average curve within ROI) is enabled (radio button Fitting Strategy – Pixel based / ROI based). + +\subsection FIT_DCE_General_models Supported models +Currently the following pharmacokinetic models for gadolinium-based contrast agent are available: +- The Descriptive Brix model \ref FIT_DCE_lit_ref1 "[1]" +- A semi-quantitative three segment linear model (3SL) +- The standard tofts model \ref FIT_DCE_lit_ref2 "[2]" +- The extended Tofts model \ref FIT_DCE_lit_ref3 "[3]" +- The two compartment exchange model (2CXM) \ref FIT_DCE_lit_ref4 "[4, 5]" + +\section FIT_DCE_Settings Model Settings +\imageMacro{dce_mri_config.png, "Example screenshot showing the config settings of the view.", 10} + +\subsection FIT_DCE_Settings_model Model specific settings +Selecting one of the \ref FIT_DCE_General_models "supported models" will open below tabs for further configuration of the model. +- The descriptive Brix model requires only definition of the duration of the bolus, i.e. the overall time of the injection (Injection Time [min]) +- The 3SL is a semi-quantitative descriptive model that distinguishes three different segments of the signal: A constant baseline, the initial fast rise (wash-in) and the final slow rise / signal decrease (washout). Each of these segments is approximated by a linear curve, with change points in-between. It requires no further configuration +- The standard Tofts model, the extended Tofts model and the 2CXM are all three compartment models that require the input of the concentration time curve in the tissue feeding artery, the AIF. In the DCE MRI Model fitting plugin, the arterial input function can be defined in several ways. For patient individual image derived AIFs, select the radio button "Select AIF from Image". In that case, a segmentation ROI for the artery has to be given to the tool (Drop-down menu AIF Mask from Data Manager). In cases, where the respective artery does not lie in the same image as the investigated tissue (e.g. in animal experiments, where a slice through the heart is used for AIF extraction), a dedicated AIF image can be selected from the Data Manager. +The other option is to define the AIF via an external file (e.g. for population derived AIFs or AIFs from blood sampling). By clicking the Browse button, one can select a csv file that holds the arterial intensity values and corresponding timepoints (in tuple format (Time, Value)). Caution: the file may not contain a header line, but the first line must start with Time and Intensity values. +Furthermore, the hematocrit level has to be set (from 0 to 1) for conversion from whole blood to plasma concentration. It is set to the literature default value of 0.45. + +\subsection FIT_DCE_Settings_start Start parameter +\imageMacro{dce_mri_start.png, "Example screen shot for start parameter settings.", 10} +In cases of noisy data it can be useful to define the initial starting values of the parameter estimates, at which optimization starts, in order to prevent optimization results in local optima. +Each model has default scalar values (applied to every voxel) for initial values of each parameter, however these can be adjusted. +Moreover, initial values can also be defined locally for each individual voxel via starting value images. + +\subsection FIT_DCE_Settings_constraint Constraint settings +\imageMacro{dce_mri_constraint.png, "Example screen shot for constraint settings.", 10} +To limit the fitting search space and to exclude unphysical/illogical results for model parameter estimates, constraints to individual parameters as well as combinations can be imposed. +Each model has default constraints, however, new ones can be defined or removed by the + and – buttons in the table. +The first column specifies the parameter(s) involved in the constraint (if multiple selected, their sum will be used) by selection in the drop down menu. +The second column defines whether the constraints defines an upper or lower boundary. +Value and Width define the actual constraint value, that should not be crossed, and a certain tolerance width. + +\subsection FIT_DCE_Settings_concentration Signal to concentration conversion settings +\imageMacro{dce_mri_concentration.png, "Example screen shot for concentration conversion settings.", 10} +Most models require concentration values as input rather than raw signal intensities (i.e. all compartment models). +The DCE MR Perfusion view offers conversion to concentration by means of relative and absolute signal enhancement as well as a special conversion for turbo flash sequences. + +\section FIT_DCE_Fitting Executing a fit +After configuration of the entire fit routine, the respective time series to be fitted and eventually the ROI mask have to be selected. +If only an image is needed, selection of the respective time series in the data manager is sufficient. +If a mask is to be selected as well, image and mask have to be selected by holding the shift key and selecting them in this order from the Data manager.\n\n + +In order to distinguish results from different model fits to the data, a Fitting name can be defined in the bottom field. +As default, the name of the model and the fitting strategy (pixel/ROI) are given. This name will then be appended by the respective parameter name.\n\n + +For development purposes and evaluation of the fits, the option "Generate debug parameter images" is available. +Enabling this option will result in additional parameter maps displaying the status of the optimizer at fit termination, like needed optimization time, number of iterations, constraint violations and reasons for fit termination (criterion reached, maximum number of iterations, etc.).\n\n + +After all necessary configurations are set, the button "Start Modelling" is enabled, which starts the fitting routine. Progress can be seen in the message box on the bottom. Resulting parameter maps will afterwards be added to the data manager as sub-nodes to the analyzed 4D image. + +\section FIT_DCE_lit References/Literature +- \anchor FIT_DCE_lit_ref1 [1] Brix G, Semmler W, Port R, Schad LR, Layer G, Lorenz WJ. Pharmacokinetic parameters in CNS Gd-DTPA enhanced MR imaging. J Comput Assist Tomogr. 1991;15:621–8. +- \anchor FIT_DCE_lit_ref2 [2] Tofts PS, Kermode AG. Measurement of the blood-brain barrier permeability and leakage space using dynamic MR imaging. 1. Fundamental concepts. Magn Reson Med. 1991;17:357–67. +- \anchor FIT_DCE_lit_ref3 [3] Sourbron SP, Buckley DL. On the scope and interpretation of the Tofts models for DCE-MRI. Magn Reson Med. 2011;66:735–45. +- \anchor FIT_DCE_lit_ref4 [4] Brix G, Kiessling F, Lucht R, Darai S, Wasser K, Delorme S, et al. Microcirculation and microvasculature in breast tumors: Pharmacokinetic analysis of dynamic MR image series. Magn Reson Med. 2004;52:420–9. +- \anchor FIT_DCE_lit_ref5 [5] Sourbron, Buckley. Tracer kinetic modelling in MRI: estimating perfusion and capillary permeability - pdf. Phys Med Biol. 2012. http://iopscience.iop.org/article/10.1088/0031-9155/57/2/R1/pdf. Accessed 1 May 2016. + -This plug-in offers the possibilities to fit several pharmacokinetic modells onto DCE MR perfusion images. */ + diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_concentration.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_concentration.png new file mode 100644 index 0000000000..5ac03206ef Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_concentration.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_config.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_config.png new file mode 100644 index 0000000000..1d6bc35cea Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_config.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_constraint.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_constraint.png new file mode 100644 index 0000000000..5ac03206ef Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_constraint.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_init.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_init.png new file mode 100644 index 0000000000..074fdd8f4a Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_init.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_start.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_start.png new file mode 100644 index 0000000000..cc77a83553 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/dce_mri_start.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/pharmacokinetics_mri_doc.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/pharmacokinetics_mri_doc.svg new file mode 100644 index 0000000000..3189376ae3 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/pharmacokinetics_mri_doc.svg @@ -0,0 +1,181 @@ + + + +image/svg+xml + + +FIT + + + + + + +MRI + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/files.cmake b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/files.cmake index d3b5a6f4ce..462c6d835d 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/files.cmake +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_MRPerfusionView_Activator.cpp MRPerfusionView.cpp ) set(UI_FILES src/internal/MRPerfusionViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_MRPerfusionView_Activator.h src/internal/MRPerfusionView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/DCEMRI.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/plugin.xml b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/plugin.xml index 672a061a8a..a724f1c486 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/plugin.xml +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/resources/DCEMRI.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/resources/DCEMRI.png deleted file mode 100644 index 3a91919a13..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/resources/DCEMRI.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/resources/icon.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/resources/icon.svg new file mode 100644 index 0000000000..6069a163d7 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/resources/icon.svg @@ -0,0 +1,174 @@ + + + +image/svg+xml + + +FIT + + + + +MRI + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/Manual.dox index 7e19a3b864..6b0075415c 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/Manual.dox @@ -1,7 +1,46 @@ /** \page org_mitk_gui_qt_pharmacokinetics_pet The Dynamic PET DataFit View -\section org_mitk_gui_qt_pharmacokinetics_pet_Overview Overview -This plug-in allows to fit dynamic PET images to different given models. +\imageMacro{pharmacokinetics_pet_doc.svg,"Icon of the DCE MR Perfusion View",3.0} + +\tableofcontents + +\section FIT_PET_Overview Overview +Pharmacokinetic analysis of concentration time curves is also of interest in the context of dynamic PET acquisition over the accumulation of a radioactive tracer in tissue. + +\section FIT_PET_Contact Contact information +This plug-in is being developed by Charlotte Debus and the SIDT group (Software development for Integrated Diagnostics +and Therapy) at the DKFZ (German Cancer Research Center). +If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. + +\subsection FIT_DCE_Cite Citation information +If you use the view for your research please cite our work as reference:\n\n +Debus C and Floca R, Ingrisch M, Kompan I, Maier-Hein K, Abdollahi A, Nolden M, MITK-ModelFit: generic open-source framework for model fits and their exploration in medical imaging – design, implementation and application on the example of DCE-MRI (arXiv:1807.07353) + +\section FIT_PET_General General information +All models require definition of the arterial tracer concentration, i.e. the AIF. For AIF definition see section 3. Instead of the hematocrit level, the whole blood to plasma correction value needs to be specified. The literature value commonly used is 0.1 +Since PET images are already in concentration units of activity per volume ([Bq/ml], translates to number of nuclei per volume), no conversion of signal intensities to concentration is offered in the plugin. If, however, conversion of the 4D images to standard uptake values (SUV) is desired, this can be performed with the separate PET SUV calculation plugin. +Start parameters and parameter constraints can be defined in the same manner as for the DCE tool. + +\subsection FIT_PET_General_models Supported models +The PET dynamic plugin works in analogy to the DCE MRI perfusion plugin. It currently supports the following compartmental models: +- One tissue compartment model (without blood volume VB) +- Extended one tissue compartment model (with blood volume VB) +- Two tissue compartment model (with blood volume) +- Two tissue compartment model for FDG (without back exchange k4) + +\section FIT_PET_Settings Model Settings + +\subsection FIT_PET_Settings_start Start parameter +In cases of noisy data it can be useful to define the initial starting values of the parameter estimates, at which optimization starts, in order to prevent optimization results in local optima. +Each model has default scalar values (applied to every voxel) for initial values of each parameter, however these can be adjusted. +Moreover, initial values can also be defined locally for each individual voxel via starting value images. + +\subsection FIT_PET_Settings_constraint Constraint settings +To limit the fitting search space and to exclude unphysical/illogical results for model parameter estimates, constraints to individual parameters as well as combinations can be imposed. +Each model has default constraints, however, new ones can be defined or removed by the + and – buttons in the table. +The first column specifies the parameter(s) involved in the constraint (if multiple selected, their sum will be used) by selection in the drop down menu. +The second column defines whether the constraints defines an upper or lower boundary. +Value and Width define the actual constraint value, that should not be crossed, and a certain tolerance width. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/pharmacokinetics_pet_doc.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/pharmacokinetics_pet_doc.svg new file mode 100644 index 0000000000..c1fbbd2d90 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/documentation/UserManual/pharmacokinetics_pet_doc.svg @@ -0,0 +1,181 @@ + + + +image/svg+xml + + +FIT + + + + + + +PET + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/files.cmake b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/files.cmake index 6ff409c29e..f606c1674f 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/files.cmake +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/files.cmake @@ -1,42 +1,42 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES org_mitk_PETDynamicView_Activator.cpp PETDynamicView.cpp ) set(UI_FILES src/internal/PETDynamicViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_PETDynamicView_Activator.h src/internal/PETDynamicView.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES - resources/PETDynamic.png + resources/icon.svg plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin set(QRC_FILES ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/plugin.xml b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/plugin.xml index 3631159e50..aaf2b2ee75 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/plugin.xml +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/plugin.xml @@ -1,12 +1,12 @@ + icon="resources/icon.svg" /> diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/resources/PETDynamic.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/resources/PETDynamic.png deleted file mode 100644 index 36aec5f5bd..0000000000 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/resources/PETDynamic.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/resources/icon.svg b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/resources/icon.svg new file mode 100644 index 0000000000..95de5f2d19 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/resources/icon.svg @@ -0,0 +1,174 @@ + + + +image/svg+xml + + +FIT + + + + +PET + + + + + \ No newline at end of file