diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox index 02b859a764..70612c9370 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox @@ -1,25 +1,25 @@ /** \bundlemainpage{org_fiberprocessing} Fiber Processing View This view provides everything needed to process fiber bundles. Available sections: - - \ref QmitkDiffusionImagingUserManualFiberManpulation - - \ref QmitkDiffusionImagingUserManualFiberProcessing + - \ref QmitkFiberProcessingUserManualFiberManpulation + - \ref QmitkFiberProcessingUserManualFiberProcessing \image html fiberprocessing.png The Fiber Processing View -\section QmitkDiffusionImagingUserManualFiberManpulation Fiber Bundle Manipulation +\section QmitkFiberProcessingUserManualFiberManpulation Fiber Bundle Manipulation Fiber extraction: Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. -\section QmitkDiffusionImagingUserManualFiberProcessing Generation of additional information from fiber bundles +\section QmitkFiberProcessingUserManualFiberProcessing Generation of additional information from fiber bundles \li Tract density image: generate a 2D heatmap from a fiber bundle \li Binary envelope: generate a binary image from a fiber bundle \li Fiber bundle image: generate a 2D rgba image representation of the fiber bundle \li Fiber endings image: generate a 2D binary image showing the locations of fiber endpoints \li Fiber endings pointset: generate a poinset containing the locations of fiber endpoints */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox index 1b924bd363..024eb4e3f3 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox @@ -1,11 +1,11 @@ /** \bundlemainpage{org_odfdetails} ODF Details View This view provides detailed information about the orentation distribution function at the current crosshair position (if a Q-Ball image is selected). A visualization of the ODF as well as the ODF values and according statistical information are displayed. \image html odfdetails.png The Gibbs Tracking View -\section QmitkDiffusionImagingUserManualInputData Issues +\section QmitkOdfDetailsUserManualInputData Issues At the moment this view can opnly process Q-Ball images but not tensor images. Also the normalization properties etc. of the image as well as the correct rotation of the ODF are currently not incorporated into the views visualization. */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox index 22722ec69a..56a9baf5bf 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox @@ -1,23 +1,23 @@ /** \bundlemainpage{org_pvanalysis} Partial Volume Analysis The "Partial Volume Analysis" view can be found in the "Quantification" perspective. It allows for robust quantification of diffusion or other scalar measures in the presents of two classes (e.g. fiber vs. non-fiber) and partial volume between them. The algorithm estimates a probabilistic segmentation of the three classes and returns a weighted average of the measure of interest within the each class. \image html pvanalysisview.png The Partial Volume Analysis View -\section QmitkDiffusionImagingUserManualInputData Export +\section QmitkPVAAnalysisUserManualExport Export All measures are automatically written to the clipboard once the estimation is updated. The histogram export is provided by the button underneath the histogram. The values can be pasted to excel or any text editor. -\section QmitkDiffusionImagingUserManualInputData Advanced Settings +\section QmitkPVAAnalysisUserManualAdvancedSettings Advanced Settings Are not recommended for use yet. -\section QmitkDiffusionImagingUserManualInputData Suggested Readings +\section QmitkPVAAnalysisUserManualSuggestedReadings Suggested Readings Diffusion tensor imaging in primary brain tumors: reproducible quantitative analysis of corpus callosum infiltration and contralateral involvement using a probabilistic mixture model. Stieltjes B, Schlüter M, Didinger B, Weber MA, Hahn HK, Parzer P, Rexilius J, Konrad-Verse O, Peitgen HO, Essig M. Neuroimage. 2006 Jun;31(2):531-42. Epub 2006 Feb 14. PMID: 16478665 */