diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberBundleOperationsViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberBundleOperationsViewUserManual.dox deleted file mode 100644 index a0b402de54..0000000000 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberBundleOperationsViewUserManual.dox +++ /dev/null @@ -1,37 +0,0 @@ -/** -\bundlemainpage{org_fiberbundleoperations} Fiber Bundle Operations View - -This view provides everything needed to process fiber bundles (mitkFiberBundle). - -Available sections: - - \ref QmitkDiffusionImagingUserManualFiberBundleManpulation - - \ref QmitkDiffusionImagingUserManualBinaryEnvelope - - \ref QmitkDiffusionImagingUserManualTdi - - \ref QmitkDiffusionImagingUserManualFiberBundleImage - - \ref QmitkDiffusionImagingUserManualFiberEndingsImage - - \ref QmitkDiffusionImagingUserManualFiberEndingsPointset - -\image html fiberbundleoperationsview.png The Fiber Bundle Operations View - -\section QmitkDiffusionImagingUserManualInputData Fiber Bundle Manipulation - -Fiber extraction: -Fiber that pass throu - -Optional Input: -\li Mask Image: Float image used as probability mask for the generation of fiber segments. Usually used as binary brain mask to reduce the searchspace of the algorithm and to avoid fibers resulting from noise outside of the brain. -\li GFA Image: Float image used to automatically determine the "particle weight" parameter. - -\section QmitkDiffusionImagingUserManualParameters Q-Ball Reconstruction - -\li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Rcommended: 10⁷-10⁹ iterations. -\li Particle length/width/weight controlling the contribution of each particle to the model M -\li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed) -\li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed). -\li Minimum fiber length constraint. Fibers containing less segments are discarded after the tracking. (usually no change needed) - -\section QmitkDiffusionImagingUserManualTrackingSurveillance Surveilance of the tracking process - -Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. - -*/ 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 new file mode 100644 index 0000000000..963ed94489 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox @@ -0,0 +1,25 @@ +/** +\bundlemainpage{org_fiberprocessing} Fiber Processing View + +This view provides everything needed to process fiber bundles. + +Available sections: + - \ref QmitkDiffusionImagingUserManualFiberManpulation + - \ref QmitkDiffusionImagingUserManualFiberProcessing + +\image html fiberbundleoperationsview.png The Fiber Processing View + +\section QmitkDiffusionImagingUserManualFiberManpulation 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 + +\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/gibbstrackingview.png b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/gibbstrackingview.png new file mode 100644 index 0000000000..3e20911bed Binary files /dev/null and b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/gibbstrackingview.png differ