diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_1.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_1.png new file mode 100644 index 0000000000..d4dabb35fb Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_1.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_2.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_2.png new file mode 100644 index 0000000000..40fe8e568e Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_2.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_3.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_3.png new file mode 100644 index 0000000000..bee492bc62 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_3.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_4.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_4.png new file mode 100644 index 0000000000..d138e18f0e Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/PreprocessingGUI_4.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingPreprocessingPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingPreprocessingPage.dox index ea1537cd97..96cabdde4f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingPreprocessingPage.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingPreprocessingPage.dox @@ -1,9 +1,26 @@ /** -\page QmitkDiffusionImagingPreprocessingPage Preprocessing of Diffusion Images +\page org_mitk_views_diffusionpreprocessing Preprocessing of Diffusion Images \section QmitkDiffusionImagingPreprocessingPagePreprocessing Preprocessing -The preprocessing view gives an overview over the important features of a diffusion weighted image like the number of gradient directions, b-value and the measurement frame. Additionally it allows the extraction of the B0 image, reduction of gradient directions and the generation of a binary brain mask. The image volume can be modified by applying a new mesurement frame, which is useful if the measurement frame is not set correctly in the image header, or by averaging redundant gradient directions. +The Preprocessing View bundles a selection of features and tools for dealing with diffusion weighted MR images. It can be used to modify header and geometry information, manipulate gradients and gradient images as well as calculating ADC maps. -\imageMacro{prepro1.png,"Preprocessing",9.97} -*/ \ No newline at end of file +\section QmitkDiffusionImagingPreprocessingPageDetails Details + +\imageMacro{PreprocessingGUI_1.png,"Gradients tab",9.97} + +The Gradients tab allows you to examine the number of b values and how many gradients were acquired for each. Here you can also visualize the gradients as points on a sphere, mirror opposite gradients so all are oriented within the same half sphere, round b values and merge similar gradients. + +\imageMacro{PreprocessingGUI_2.png,"Image values tab",9.97} + +The Image values tab enables you to manipulate the voxel values by e.g. resampling images, averaging repetitions of the same gradient, normalizing the image values or merging several DWIs into one. + +\imageMacro{PreprocessingGUI_3.png,"Header tab",9.97} + +In the Header tab you can selectively change geometry information of the image and delete or extract specific gradient volumes. + +\imageMacro{PreprocessingGUI_4.png,"Other tab",9.97} + +Miscellaneous tools in the Other tab allow for ADC map calculation and the extraction of the b0 image with the possibility of averaging all b0 images. + +*/ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingRegistration.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingRegistration.dox index 354700a564..771863b4ba 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingRegistration.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingRegistration.dox @@ -1,16 +1,16 @@ /** -\page QmitkDiffusionImagingDWIRegistrationPage DWI Registration +\page org_mitk_views_diffusionregistrationview DWI Registration \section QmitkDiffusionImagingUserManualDWIRegistration DWI Registration The DWI registration view allows head-motion and eddy-current correction. First the b=0 images (if more than 1) are registered and averaged. The averaged image then serves as fixed image for the alignment of the remaining (weighted, b>0) images. \imageMacro{registration_basic.png,"Basic DWI Registration Interface",8.00} In the basic settings, a selected DW image in the Data Manager is marked as Input Data and the Start Head Motion Correction button is enabled. If more than one DW images are selected, they will be processed in a consecutive manner. For larger sets of dw images to be processed, the Advanced settings can be used. \imageMacro{registration_batch.png,"Batch Processing DWI Registration Interface",8.00} Here all valid .dwi data located in the given input folder will be processed through the head motion correction and the output will be stored in the current working directory or in a custom folder if specified in the user interface. The output image will have the _MC postfix attached to the input's name. -*/ \ No newline at end of file +*/ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingVisualization.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingVisualization.dox index eff05db5ed..cc1e7156ce 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingVisualization.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkDiffusionImagingVisualization.dox @@ -1,19 +1,19 @@ /** -\page QmitkDiffusionImagingVisualization ODF Visualization +\page org_mitk_views_controlvisualizationpropertiesview ODF Visualization \section QmitkDiffusionImagingVisualizationSettings ODF Visualization Setting In this small view, the visualization of ODFs and diffusion images can be configured. Depending on the selected image in the data storage, different options are shown here. For tensor or q-ball images, the visibility of glyphs in the different render windows (T)ransversal, (S)agittal, and (C)oronal can be configured here. The maximal number of glyphs to display can also be configured here for. This is usefull to keep the system response time during rendering feasible. The other options configure normalization and scaling of the glyphs. In diffusion images, a slider lets you choose the desired image channel from the vector of images (each gradient direction one image) for rendering. Furthermore reinit can be performed and texture interpolation toggled. This is how a visualization with activated glyphs should look like: \imageMacro{visualization3.png,"Q-ball image with ODF glyph visibility toggled ON",16.00} */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkOdfDetailsViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkOdfDetailsViewUserManual.dox index 96495480d4..257071dffa 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkOdfDetailsViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/QmitkOdfDetailsViewUserManual.dox @@ -1,8 +1,8 @@ /** \page org_mitk_views_odfdetails ODF Details View This view provides detailed information about the orentation distribution function at the current crosshair position (if a Tensor/Q-Ball image is selected). A visualization of the ODF as well as statistical information are displayed. -\imageMacro{odfdetails.png,"The Gibbs Tracking View",10.01} +\imageMacro{odfdetails.png,"The ODF Details View",10.01} */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/prepro1.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/prepro1.png deleted file mode 100644 index 90b679ee66..0000000000 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Preproc_Recons/prepro1.png and /dev/null 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 0ba46fa6f0..f61238e231 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 QmitkDiffusionImagingDWIRegistrationPage - \li \subpage QmitkDiffusionImagingPreprocessingPage + \li \subpage org_mitk_views_diffusionregistrationview + \li \subpage org_mitk_views_diffusionpreprocessing \li \subpage QmitkDiffusionImagingReconstructionPage - \li \subpage QmitkDiffusionImagingVisualization + \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_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. -*/ \ No newline at end of file +*/