Documentation/Nightly/Modules/TractographyDisplay

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Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website. Author: Isaiah Norton, Goldby Lab Author: Demian Wassermann, SPL Contributor1: Steve Pieper, Isomics Inc. Contributor2: Alex YarmarKovich, Isomics Inc. Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email>

SlicerDMRI   Surgical Planning Laboratory   NAC   Tractography displayed in line, tube and glyphs   Tractography displayed on slices

Module Description

Allows the user to manipulate several different characteristics of the traced white matter tracts. Examples are: change of color; display of the fractional anisotropy along the tract; display of the tracts as tubes or lines; interactive selection of the tracts; and cropping.

Use Cases

Most frequently used for these scenarios:

• Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
• Use Case 2: Display the tracts as lines or tubes
• Use Case 3: Interactive selection or cropping of a certain bundle.

Tutorials

Links to tutorials that use this module

• Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial

Panels and their use

Line: Display the tracts as lines Tube: Display the tracts as tubes Slice Intersection: Show the tracts in the 2D view Glyph: Display glyphs representing the diffusion tensors along the tracts Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance. Fiber Bundle Selection: Perform interactive selection and cropping of the tracts ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts Disable/Positive/Negative ROI: Set the selection mode to Select everything; Select the tracts traversing the ROI; Select the tracts not traversing the ROI Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones Advance Display: For the lines, tubes and glyphs Visibility: Toggle the visibility of the bundle Opacity: Change the transparency level of the bundle Color By: Change the way the bundle is colored; either by a tensor-derived property or by a group id Solid Color: Color the bundle of a single solid color References Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation Information for Developers