diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 2bb8e351e4..b567c4c83e 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,84 +1,84 @@ /** \page PluginListPage MITK Plugin Manuals 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. \subpage PluginListGeneralPage \subpage PluginListSpecificPage */ diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox index 8be8a5f620..ef1ea02159 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox @@ -1,45 +1,45 @@ /** \page PluginListSpecificPage List of Application-specific Plugins \li \subpage org_mitk_gui_qt_aicpregistration \li \subpage org_mitk_gui_qt_cest \li \subpage org_mitk_gui_qt_classificationsegmentation \li \subpage org_mitk_gui_qt_flowapplication \li \subpage org_mitk_views_cmdlinemodules - \li \subpage org_mitk_gui_qt_pharmacokinetics_concentration_mri + \li \subpage org_mitk_views_pharmacokinetics_concentration_mri \li \subpage org_mitk_views_pharmacokinetics_mri \li \subpage org_mitk_gui_qt_pharmacokinetics_pet \li \subpage org_mitk_gui_qt_eventrecorder \li \subpage org_mitk_gui_qt_examples \li \subpage org_mitk_gui_qt_geometrytools \li \subpage org_mitk_gui_qt_igtexample \li \subpage org_mitk_gui_qt_igtlplugin \li \subpage org_mitk_gui_qt_igttracking \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement \li \subpage org_mitk_views_imagestatistics \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_fit_demo \li \subpage org_mitk_gui_qt_fit_genericfitting \li \subpage org_mitk_gui_qt_fit_inspector \li \subpage org_mitkexamplesopencv \li \subpage org_mitk_gui_qt_overlaymanager \li \subpage org_mitk_gui_qt_mitkphenotyping \li \subpage org_mitk_gui_qt_photoacoustics_pausmotioncompensation \li \subpage org_mitk_example_gui_pcaexample \li \subpage org_mitk_gui_qt_preprocessing_resampling \li \subpage org_mitk_gui_qt_pharmacokinetics_curvedescriptor \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_gui_qt_pharmacokinetics_simulation \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_renderwindowmanager \li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing \li \subpage org_mitk_gui_qt_spectrocamrecorder \li \subpage org_surfacematerialeditor \li \subpage org_blueberry_ui_qt_objectinspector \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_ultrasound \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_mitk_gui_qt_xnat */ \ No newline at end of file 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 79c3c04ad5..7c16b548b7 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 @@ -1,16 +1,35 @@ /** -\page org_mitk_gui_qt_pharmacokinetics_concentration_mri The Concentration Curve Converter View +\page org_mitk_views_pharmacokinetics_concentration_mri The DCE Concentration Curve Converter View -\imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the Concentration Curve Converter View",3.0} +\imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the DCE Concentration Curve Converter View",3.0} \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_views_pharmacokinetics_concentration_mri_overview Overview +This view offers a dedicated tool for the conversion of DCE MR image signal intensities to contrast agent (CA) concentration. +It contains a subset of the conversion tools for T1-weighted signal intensities, which are a part of the DCE MR Perfusion Datafit View (see \ref FIT_DCE_Settings_concentration). +Additionally, it allows for the conversion between T2-weighted MR signal intensities and contrast agent concentration. -\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 German Cancer Research Center (DKFZ). +\section org_mitk_views_pharmacokinetics_concentration_mri_Contact Contact information 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 org_mitk_views_pharmacokinetics_concentration_mri_T1_conversion Conversion of T1-weighted MRI data + +\imageMacro{concentration_curve_converter_T1_weighted4D.png,"Example screenshot of the conversion of T1-weighted MR images",3.0} +The view offers the choice between a 3D Image and a 4D image. If a 4D image is selected, the Selected Time Series needs to be specified. +In this case, the baseline image is automatically extracted as the first time point image of the time series. +In case of a 3D image to be converted, additionally to the selected 3D image a Baseline Image (without CA) has to be specified.\n\n + +In the configuration section, the following types of conversion can be chosen: +- Absolute Signal Enhancement: The contrast agent concentration c is calculated according to the formula: c = k*(S(t)-S(0)), where S(t) is the dynamic T1-weighted signal intensity, S(0) the baseline signal and k a user-defined conversion factor. +- Relative Signal Enhancement: The contrast agent concentration c is calculated according to the formula: c = k*(S(t)-S(0))/S(0), where S(t) is the dynamic T1-weighted signal intensity, S(0) the baseline signal and k a user-defined conversion factor. +- Turbo FLASH Sequence: The conversion from signal S(t) to contrast agent concentration c is calculated according to the turboFLASH (ultrafast gradient echo) sequence specific formula. + + +\section org_mitk_views_pharmacokinetics_concentration_mri_T2_conversion Conversion of T2-weighted MRI data +\imageMacro{concentration_curve_converter_T2_weighted.png,"Example screenshot of the conversion of T2-weighted MR images",3.0} + +The contrast agent concentration c is calculated according to the formula: c = -k/TE*ln(S(t)/S(0)), where S(t) is the dynamic T2-weighted signal intensity, S(0) the baseline signal, k a user-defined conversion factor and TE the echo time of the employed sequence. +In practice, the factor k is often set to unity. + */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png new file mode 100644 index 0000000000..ef521cc592 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png new file mode 100644 index 0000000000..cd4158f49d Binary files /dev/null and b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png differ 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 ca8c8a0fe5..0e19a70b02 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 @@ -