diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox index f45873f60f..9c1e982b69 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox @@ -1,28 +1,23 @@ /** \page org_fiberprocessing Fiber Processing View This view provides everything needed to process fiber bundles. -Available sections: - - \ref QmitkFiberProcessingUserManualFiberManpulation - - \ref QmitkFiberProcessingUserManualFiberProcessing - \image html fiberprocessing.png The Fiber Processing View -\section QmitkFiberProcessingUserManualFiberManpulation Fiber Bundle Modification - 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. This can also be done using 3D ROIs represented as closed surface meshes. +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. The extraction can also be performed using 3D ROIs represented as closed surface meshes. In this extraction method, the logical operations are not implemented at the moment. -\section QmitkFiberProcessingUserManualFiberProcessing Fiber Bundle Processing +The selected fiber bundle can be smoothed by interpolating the fiber points using Kochanek splines with the specified number of points per cm. +If a float image with pixel values between 0 and 1 is selcted, the fiber bundle can be colored according to the pixel values. + +Generation of additional data 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 -The selected fiber bundle can be smoothed by interpolating the fiber points using Kochanek splines with the specified number of points per cm. -If a float image with pixel values between 0 and 1 is selcted, the fiber bundle can be colored according to the pixel values. */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox index e7098f064f..7885ebd5dc 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox @@ -1,11 +1,8 @@ /** \page 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. +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. \image html odfdetails.png The Gibbs Tracking View -\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/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox index ccb460739d..7573738c5e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox @@ -1,34 +1,31 @@ /** \page org_stochastictracking Stochastic Tracking View This view provides the user interface for the Stochastic Fibertracking algorithm, proposed by Ngo [1]. Available sections: - \ref QmitkStochasticTrackingUserManualInputData - \ref QmitkStochasticTrackingUserManualParameters - \ref QmitkStochasticTrackingUserManualReferences \image html stochastictrackingview.png Stochastic Tracking View \section QmitkStochasticTrackingUserManualInputData Input Data Mandatory Input: -\li For a successful execution of the stochastic tractography filter, a DWI input and a binary image defining the desired ROI are required. The ROI serves as the origin from where on the fibers are beeing tracked. Both, DWI and ROI data can be imported via drag nŐ drop or via the opening dialog box provided by MITK. Alternatively, the segmentation view offers tools for generating ROI data. \li One DWI Image image selected in the datamanager \li One or more ROIs selected in the datamanager +For a successful execution of the stochastic tractography filter, a DWI input and a binary image defining the desired ROI are required. The ROI serves as the origin from where on the fibers are beeing tracked. To generate the seed ROI the segmentation view in the quantification perspective can be used or a binary image can be loaded. \section QmitkStochasticTrackingUserManualParameters Input Parameters - -\li Parameters such as max. tract length (Tract_len), number of total tracts per voxel (TotalTracts) and likelihood cache size in MB (Lkhd chache) are individually set by the user. - +\li Parameters such as max. tract length, number of seeds per voxel and likelihood cache size in MB can be controlled individually. \li After successfully setting necessary Input and Parameter, pressing the command button executes the algorithm. - \section QmitkStochasticTrackingUserManualReferences References [1] Tri M. Ngo, Polina Golland, and Tri M. Ngo. A stochastic tractography system and applications, 2007 */