diff --git a/Documentation/Doxygen/UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/UserManual/MITKPluginManualsList.dox index be03f2ba30..1b70e25a7f 100644 --- a/Documentation/Doxygen/UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/UserManual/MITKPluginManualsList.dox @@ -1,46 +1,45 @@ /** \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_diffusionimaging \li \subpage org_mitk_views_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_mitk_gui_qt_measurementtoolbox - \li \subpage org_mitk_views_meshdecimation \li \subpage org_mitk_views_moviemaker \li \subpage org_mitk_views_screenshotmaker \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_gui_qt_python \li \subpage org_mitk_gui_qt_registration \li \subpage org_mitk_gui_qt_remeshing \li \subpage org_mitk_views_segmentation \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 \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_blueberry_ui_qt_objectinspector \li \subpage org_mitk_gui_qt_eventrecorder */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/DataImport/dicom1.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/DataImport/dicom1.png index 0151f56bea..85ca20974f 100644 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/DataImport/dicom1.png and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/DataImport/dicom1.png differ diff --git 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b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/visualization3.png index acc816f8d7..1f0a0fd15b 100644 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/visualization3.png and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/visualization3.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox index f61238e231..571689e8e1 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox @@ -1,84 +1,84 @@ /** \page org_mitk_gui_qt_diffusionimaging MITK Diffusion Imaging (MITK-DI) \tableofcontents This module provides means to diffusion weighted image reconstruction, visualization and quantification. Diffusion tensors as well as different q-ball reconstruction schemes are supported. Q-ball imaging aims at recovering more detailed information about the orientations of fibers from diffusion MRI measurements and, in particular, to resolve the orientations of crossing fibers. \section org_mitk_gui_qt_diffusionimagingComponents Components MITK Diffusion consists of further components, which have their own documentation, see: \subsection org_mitk_gui_qt_diffusionimagingComponentsDataImport Data Import \li \subpage QmitkDiffusionImagingDataImportPage \subsection org_mitk_gui_qt_diffusionimagingComponentsPreprocessingAndReconstruction Preprocessing and Reconstruction Register or denoise original data and convert it into tensor or q-ball images. \li \subpage org_mitk_views_diffusionregistrationview \li \subpage org_mitk_views_diffusionpreprocessing \li \subpage QmitkDiffusionImagingReconstructionPage \li \subpage org_mitk_views_controlvisualizationpropertiesview \li \subpage org_mitk_views_odfdetails \li \subpage org_mitk_views_odfmaximaextraction \li \subpage org_mitk_views_denoisingview \subsection org_mitk_gui_qt_diffusionimagingComponentsFiberTracking Fiber Tracking Create and work with fiber tractographies. \li \subpage org_mitk_views_fiberprocessing \li \subpage org_mitk_views_gibbstracking \li \subpage org_mitk_views_stochasticfibertracking \li \subpage org_mitk_views_fiberextraction \li \subpage org_mitk_views_fiberprocessing \li \subpage org_mitk_views_streamlinetracking \li \subpage org_mitk_views_fiberfoxview \li \subpage org_mitk_views_fieldmapgenerator \subsection org_mitk_gui_qt_diffusionimagingComponentsQuantification Quantification Create parameter maps and quantify different properties. - \li \subpage QmitkDiffusionImagingQuantificationPage + \li \subpage org_mitk_views_diffusionquantification \li \subpage org_mitk_views_ivim \li \subpage org_mitk_views_partialvolumeanalysisview \li \subpage org_mitk_views_tractbasedspatialstatistics \subsection org_mitk_gui_qt_diffusionimagingComponentsConnectomics Connectomics Create and analyse connectome networks. \li \subpage org_mitk_diffusionimagingapp_perspectives_connectomics \section org_mitk_gui_qt_diffusionimagingIssues Known Issues \li Dicom Import: The dicom import has so far only been implemented for Siemens dicom images. MITK-DI is capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. \section org_mitk_gui_qt_diffusionimagingTechnicalDetails Technical Information for Developers The diffusion imaging module uses additional properties beside the ones in use in other modules, for further information see \ref DiffusionImagingPropertiesPage . \section org_mitk_gui_qt_diffusionimagingReferences References Further reading regarding diffusion: 1. http://teem.sourceforge.net/nrrd/format.html 2. http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format 3. C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis, "Processing and visualization for Diffusion tensor MRI", Medical image Analysis, 2002, pp 93-108 5. Tuch, D.S., 2004. Q-ball imaging. Magn Reson Med 52, 1358-1372. 6. Descoteaux, M., Angelino, E., Fitzgibbons, S., Deriche, R., 2007. Regularized, fast, and robust analytical Q-ball imaging. Magn Reson Med 58, 497-510. 7. Aganj, I., Lenglet, C., Sapiro, G., 2009. ODF reconstruction in q-ball imaging with solid angle consideration. Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging Boston, MA. 8. Goh, A., Lenglet, C., Thompson, P.M., Vidal, R., 2009. Estimating Orientation Distribution Functions with Probability Density Constraints and Spatial Regularity. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv LNCS 5761, 877 ff. 9. J.-D. Tournier, S. Mori, A. Leemans., 2011. Diffusion Tensor Imaging and Beyond. Magn Reson Med 65, 1532-1556. */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/QmitkDiffusionImagingQuantificationPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/QmitkDiffusionImagingQuantificationPage.dox index c3ca35f105..cec142beed 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/QmitkDiffusionImagingQuantificationPage.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/QmitkDiffusionImagingQuantificationPage.dox @@ -1,8 +1,8 @@ /** -\page QmitkDiffusionImagingQuantificationPage Quantification +\page org_mitk_views_diffusionquantification Scalar Indices -The quantification view allows the derivation of different scalar anisotropy measures for the reconstructed tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or q-balls (Generalized Fractional Anisotropy). +The scalar indices view allows the derivation of different scalar anisotropy measures for the reconstructed tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or q-balls (Generalized Fractional Anisotropy). -\imageMacro{quantification.png,"Anisotropy quantification",2} -*/ \ No newline at end of file +\imageMacro{ScalarIndicesGUI.png,"Anisotropy quantification",2} +*/ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/ScalarIndicesGUI.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/ScalarIndicesGUI.png new file mode 100644 index 0000000000..e3688f56cc Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/ScalarIndicesGUI.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/quantification.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/quantification.png deleted file mode 100644 index a768b66dca..0000000000 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Quantification/quantification.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox index 9f679c8296..dad1bdf580 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox @@ -1,10 +1,10 @@ /** \page org_mitk_gui_qt_diffusionimagingapp Using The Diffusion Imaging Application \section QMitkDiffusionApplicationManualOverview What is the Diffusion Imaging Application -The Diffusion Imaging Application contains selected views for the analysis of images of the human brain. These encompass the views developed by the Neuroimaging Group of the Division Medical and Biological Informatics as well as basic image processing views such as segmentation and volumevisualization. +The Diffusion Imaging Application contains selected views for the analysis of images of the human brain. These encompass the views developed by the Medical Image Computing Group of the Division Medical and Biological Informatics as well as basic image processing views such as segmentation and volumevisualization. For a basic guide to MITK see \ref MITKUserManualPage . */