Difference between revisions of "Documentation/4.0/Modules/TractographyDisplay"

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Author: Isaiah Norton, Goldby Lab<br>
 
Author: Isaiah Norton, Goldby Lab<br>
 
Author: Demian Wassermann, SPL<br>
 
Author: Demian Wassermann, SPL<br>
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Contributor1: Steve Pieper, Isomics<br>
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Contributor1: Steve Pieper, Isomics Inc.<br>
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Contributor1: Alex Yarmanovich, Isomics<br>
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Contributor2: Alex YarmarKovich, Isomics Inc.<br>
 
Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
 
Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
 
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Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
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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.
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Most frequently used for these scenarios:
 
Most frequently used for these scenarios:
  
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* Use Case 1:
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* Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
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* Use Case 2:
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* Use Case 2: Display the tracts as lines or tubes
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* Use Case 3: Interactive selection or cropping of a certain bundle.
  
 
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A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:
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[[image:2011-11-12-CroppingWholeBrainTractography.png|400px]]
  
 
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* Input panel1:
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*  
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** First input
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** Line: Display the tracts as lines
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** Second input
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** Tube: Display the tracts as tubes
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* Parameters panel:
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*** Slice Intersection: Show the tracts in the 2D view
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** First parameter
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** Glyph: Display glyphs representing the diffusion tensors along the tracts
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** Second parameter
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** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
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* Output panel:
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* Fiber Bundle Selection: Perform interactive selection and cropping of the tracts
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** First output
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** ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts
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** Second output
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** Disable/Positive/Negative ROI: Set the selection mode to '''Select everything'''; '''Select the tracts traversing the ROI'''; '''Select the tracts not traversing the ROI'''
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* Viewing panel:
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** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
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** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
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* Advance Display: For the lines, tubes and glyphs
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** Visibility: Toggle the visibility of the bundle
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** Opacity: Change the transparency level of the bundle
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** Color By: Change the way the bundle is colored; either by a tensor-derived property or by a group id
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** Solid Color: Color the bundle of a single solid color
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Using this later template, the final syntax would be:
 
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Latest revision as of 07:30, 14 June 2013

Home < Documentation < 4.0 < 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.

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

Work in progress
 Section under construction.


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