Documentation/4.3/Modules/TractographyDisplay

For the latest Slicer documentation, visit the read-the-docs.

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>

Surgical Planning Laboratory

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.
• Use Case 4: Interactive editing (selecting/deleting) or cropping of a certain bundle.

Tutorials

Links to tutorials that use this module

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