Documentation/4.3/Modules/TractographyDisplay

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For the latest Slicer documentation, visit the 4.10 page.


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

TractographyDisplayModule.PNG

  • Simple Fiber Bundle Display Control panel
    • Solid Tube Color: toggles on/off solid color for tubes
    • Name: click to make a fiber bundle active
    • Lines: Display the tracts as lines
    • Tubes: Display the tracts as tubes
    • Tubes Slices: Show the tracts intersection with slice planes in the 2D views
    • Glyphs: Display glyphs representing the diffusion tensors along the tracts
    • Tubes Color: Select solid color for tubes
    • 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
    • Interactive ROI: toggles on/off the interactive updates during manipulating the ROI
    • ROI Visibility: toggles on/off the selected ROI's visibility
    • Extract 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
    • Enable Interactive Edit: Enables individual fiber selection/deletion. First click in 3D view to focus, then use:
      • 's' to toggle selecting/unselecting of the individual fiber under the mouse
      • 'd' for deleting all selected fibers or of the individual fiber under the mouse
      • 'x' for unselecting all selected fibers
  • 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