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/QmitkGibbsTrackingViewUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox new file mode 100644 index 0000000000..247a462d9a --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox @@ -0,0 +1,40 @@ +/** +\bundlemainpage{org_gibbstracking} Gibbs Tracking View + +This view provides the user interface for the Gibbs Tracking algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1]. + +Available sections: + - \ref QmitkDiffusionImagingUserManualInputData + - \ref QmitkDiffusionImagingUserManualParameters + - \ref QmitkDiffusionImagingUserManualTrackingSurveillance + - \ref QmitkDiffusionImagingUserManualReferences + +\image html gibbstrackingview.png The Gibbs Tracking View + +\section QmitkDiffusionImagingUserManualInputData Input Data + +Mandatory Input: +\li One Q-Ball image selected in the datamanager + +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. + +\section QmitkDiffusionImagingUserManualReferences References + +[1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962 + + +*/ 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 new file mode 100644 index 0000000000..f7caec3ddd --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox @@ -0,0 +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 odfdetailsview.png The Gibbs Tracking View + +\section QmitkDiffusionImagingUserManualInputData 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/fiberprocessing.png b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fiberprocessing.png new file mode 100644 index 0000000000..595de7ff23 Binary files /dev/null and b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fiberprocessing.png differ 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 diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/odfdetails.png b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/odfdetails.png new file mode 100644 index 0000000000..59ac0b25f6 Binary files /dev/null and b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/odfdetails.png differ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui index 09310af2be..ae5717430c 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui @@ -1,535 +1,544 @@ QmitkFiberProcessingViewControls 0 0 665 587 Form - + + 5 + + + 0 + + + 5 + + 0 0 0 200 50 300 60 QFrame::NoFrame QFrame::Raised 12 0 30 30 Draw circular ROI :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true 30 30 Draw rectangular ROI :/QmitkDiffusionImaging/rectangle.png:/QmitkDiffusionImaging/rectangle.png 32 32 true true 30 30 Draw polygonal ROI :/QmitkDiffusionImaging/polygon.png:/QmitkDiffusionImaging/polygon.png 32 32 true true Qt::Horizontal 40 20 16777215 16777215 QFrame::NoFrame QFrame::Raised 0 0 false 60 16777215 Create AND composition with selected ROIs AND false 60 16777215 Create OR composition with selected ROIs OR false 60 16777215 Create NOT composition from selected ROI NOT QFrame::NoFrame QFrame::Raised 0 false 0 0 200 16777215 11 Extract fibers passing through selected ROI or composite ROI Extract from ROIs false 0 0 200 16777215 11 Merge two fiber bundles Join Bundles false 0 0 300 16777215 11 Generate a binary image containing all selected ROIs Generate ROI Image false 0 0 200 16777215 11 Returns fiber bundle containing all fibers the two selected bundles dont't have in common Substract Bundles 0 0 QFrame::StyledPanel QFrame::Raised Fibers in Selected Bundle: 0 QFrame::StyledPanel QFrame::Raised 0 0 Tract Density Image (TDI) Binary Envelope Fiber Bundle Image Fiber Endings Image Fiber Endings Pointset Upsampling Factor 1 10 4 false 0 0 200 16777215 11 Perform selected operation on fiber bundle Generate If selected operation generates an image, the inverse image is returned Invert Qt::Vertical 20 40