diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox new file mode 100644 index 0000000000..c9079c01b6 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox @@ -0,0 +1,35 @@ +/** +\page org_mitk_views_fiberfox Fiberfox + +This view provides the user interface for Fiberfox, an interactive simulation tool for the generation of complex white matter tissue models and corresponding DW-MRI. Arbitrary fiber configurations like bended, crossing, kissing, twisting, and fanning bundles can be intuitively defined by positioning only a few 3D waypoints to trigger the automated generation of synthetic fibers. From these fibers, a DW-MRI signal is simulated according to the specified acquisition settings such as gradient direction, b-value, signal-to-noise ratio, image size, and resolution. Fiberfox incorporates different models of diffusion, noise, and artifacts to simulate realistic images. + +Available sections: + - \ref QmitkGibbsTrackingUserManualFiberDefinition + - \ref QmitkGibbsTrackingUserManualSignalGeneration + - \ref QmitkGibbsTrackingUserManualReferences + +\image html fiberfoxview.png Screenshot of the Fiberfox framework. The four render windows display an axial, sagittal and coronal 2D cut as well as a 3D view of a synthetic fiber helix and the fiducials used to define its shape. In the 2D views the helix is superimposing the baseline volume of the corresponding diffusion weighted image. The sagittal render window shows a closeup view on one of the circular fiducials. + +\section QmitkGibbsTrackingUserManualFiberDefinition Fiber Definition + +Fiber strands are defined simply by placing markers in a 3D image volume. The fibers are then interpolated between these fiducials. + +Example: +\li Chose an image volume to place the markers used to define the fiber pathway. If you don't have such an image available switch to the "Image Generation" tab, define the size and spacing of the desired image ang click "Generate Image". If no fiber bundle is selected, this will generate a dummy image that can be used to place the fiducials. +\li Start placing fiducials at the desired positions to define the fiber pathway. To do that, click on the button with the circle pictogram, then click at the desired position and plane in the image volume and drag your mouse while keeping the button pressed to generate a circular shape. Adjust the shape using the control points. The position of the control point with the attached line connecting it to the center of the fiducial introduces a twist of the fibers between two successive fiducials. The actual fiber generation is triggered automatically as soon as you place the third control point. +\li In some cases the fibers are entangled in a way that can't be resolved by introducing an additional fiber twist. Fiberfox tries to avoid these situations, which arise from different normal orientations of succeeding fiducials, automatically. In rare cases this is not successful. Use the PICTURE button to flip the fiber positions of the selected fiducial in one dimension. Either the problem is resolved now or you can resolve it manually by adjusting the twist-control point. + +Parameters: +If not self explanatory please refer to TODO. + +\section QmitkGibbsTrackingUserManualSignalGeneration Image Generation + +Fiberfox uses a ball-zeppelin model to generate the artificial signal. For details about the signal generation process please refer to TODO. +A diffusion weighted image is generated from the fibers by selecting the according fiber bundle in the datamanager and clicking "Generate Image". Additionally to the fiber bundle a binary mask can be specified that defines the tissue area. Voxels outside of this mask will contain no signal, only noise. If no tissue mask is selected, the whole image volume is regarded as tissue. Fiberfox allows the addition of artifcats often present in EPI based diffusion weighted datasets like rician noise, Gibbs ringing and blurring introduced by the T2 signal decay. + +Parameters: +\li TODO + +If you want to use the same parameters (b-value, gradient directios, image geometry) as used for an already acquired dataset, simply select it additionally to the other input nodes. Fiberfox will automatically use these parameters for the signal generation. + +*/