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

Panels and their use

2011-11-12-CroppingWholeBrainTractography.png

    • 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