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

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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 [http://www.na-mic.org/ NA-MIC website].<br>
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Author: Isaiah Norton, Goldby Lab<br>
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Title: Tractography Display
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Author: Demian Wassermann, SPL<br>
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Contributor1: Steve Pieper, Isomics Inc.<br>
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Author(s)/Contributor(s): Demian Wassermann, Isaiah Norton, Lauren O'Donnell, Steve Pieper, Alex Yarmarkovich (SPL, LMI, BWH, SlicerDMRI)
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Contributor2: Alex YarmarKovich, Isomics Inc.<br>
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Contact:  Demian Wassermann, <email>demian@bwh.harvard.edu</email><br>
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License: 3D Slicer Contribution and Software License Agreement
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Acknowledgements: The SlicerDMRI developers gratefully acknowledge funding for this project provided by NIH NCI ITCR U01CA199459 (Open Source Diffusion MRI Technology For Brain Cancer Research), NIH P41EB015898 (National Center for Image-Guided Therapy) and NIH P41EB015902 (Neuroimaging Analysis Center), as well as 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.
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Contact:  slicer-users@bwh.harvard.edu
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Website: http://slicerdmri.github.io/
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|Image:SlicerDMRIScreenshot.jpg|SlicerDMRI
 
|Image:Logo-splnew.jpg|Surgical Planning Laboratory
 
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|Image:NAC-logo.png|NAC
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|Image:Tracts display.png|Tractography displayed in line, tube and glyphs
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|Image:Tracts on slices.png|Tractography displayed on slices
 
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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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Allows the user to modify the display of diffusion tractography. 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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Links to tutorials that use this module
 
Links to tutorials that use this module
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* Slicer4 Diffusion Tensor Imaging Tutorial: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial <!-- ---------------------------- -->
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*  
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* Simple Display
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** Line: Display the tracts as lines
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** Solid Tube Color: Display the tracts as tubes in solid color, if checked
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** Tube: Display the tracts as tubes
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** Lines: Display the tracts as lines
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*** Slice Intersection: Show the tracts in the 2D view
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** Tubes: Display the tracts as tubes
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** Glyph: Display glyphs representing the diffusion tensors along the tracts
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** Tubes Slice: Show the tracts in the 2D view (Tubes Slice)
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** Glyphs: Display glyphs representing the diffusion tensors along the tracts
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** Tubes: Specify the solid tube color
 
** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
 
** Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
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* Fiber Bundle Selection: Perform interactive selection and cropping of the tracts
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* Fiber Bundle Selection: Perform selection and cropping of the tracts
 
** ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts
 
** ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts
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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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** Disable/Positive/Negative ROI: Set the selection mode to ''Select everything'', ''Select the tracts traversing the ROI'' or ''Select the tracts not traversing the ROI''
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** Create Bundle From ROI: Create a new fiber bundle which contains only the selected ones
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** Interactive ROI: Allow the fiber selection and cropping in an interactive way
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** ROI Visibility: Display the ROI
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** Extract Bundle From ROI: Extract a new fiber bundle which contains only the selected ones
 
** Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
 
** 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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*** Confirm update: Confirm update given the ROI
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** Enable Interactive Edit: Allow to edit the ROI in an interactive way
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* Advanced Display: For the lines, tubes and glyphs
 
** Visibility: Toggle the visibility of the bundle
 
** Visibility: Toggle the visibility of the bundle
 
** Opacity: Change the transparency level of the bundle
 
** 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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** Fiber Bundle Coloring: Change the way the bundle is colored, one of "Of Tensor Property", "Of Scalar Value", "Color Fibers By Mean Orientation", "Color Fibers By Segment Orientation", "Of Fiber Cluster Group ID" or "Solid Color".
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** Solid Color: Color the bundle of a single solid color
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*** Auto W/L: Adjust the window level automatically
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** Material Properties: Adjust Color, Opacity, Ambient, Diffuse, Specular, Power and Backface Culling of the displayed tracts.
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*** Preview: Color preview given the adjusted properties
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*** Presents: Select one of the predefined property sets
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Publications related to this module go here. Links to pdfs would be useful.
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*  http://slicerdmri.github.io/
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For extensions: link to the source code repository and additional documentation
 
  
 
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Latest revision as of 13:15, 27 November 2019

Home < Documentation < Nightly < Modules < TractographyDisplay


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


Introduction and Acknowledgements

Title: Tractography Display

Author(s)/Contributor(s): Demian Wassermann, Isaiah Norton, Lauren O'Donnell, Steve Pieper, Alex Yarmarkovich (SPL, LMI, BWH, SlicerDMRI)

License: 3D Slicer Contribution and Software License Agreement

Acknowledgements: The SlicerDMRI developers gratefully acknowledge funding for this project provided by NIH NCI ITCR U01CA199459 (Open Source Diffusion MRI Technology For Brain Cancer Research), NIH P41EB015898 (National Center for Image-Guided Therapy) and NIH P41EB015902 (Neuroimaging Analysis Center), as well as 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.

Contact: slicer-users@bwh.harvard.edu

Website: http://slicerdmri.github.io/

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


Module Description

Allows the user to modify the display of diffusion tractography. 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

  • Simple Display
    • Solid Tube Color: Display the tracts as tubes in solid color, if checked
    • Lines: Display the tracts as lines
    • Tubes: Display the tracts as tubes
    • Tubes Slice: Show the tracts in the 2D view (Tubes Slice)
    • Glyphs: Display glyphs representing the diffusion tensors along the tracts
    • Tubes: Specify the solid tube color
    • Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance.
  • Fiber Bundle Selection: Perform 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 or Select the tracts not traversing the ROI
    • Interactive ROI: Allow the fiber selection and cropping in an interactive way
    • ROI Visibility: Display the ROI
    • Extract Bundle From ROI: Extract a new fiber bundle which contains only the selected ones
    • Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones
      • Confirm update: Confirm update given the ROI
    • Enable Interactive Edit: Allow to edit the ROI in an interactive way
  • Advanced Display: For the lines, tubes and glyphs
    • Visibility: Toggle the visibility of the bundle
    • Opacity: Change the transparency level of the bundle
    • Fiber Bundle Coloring: Change the way the bundle is colored, one of "Of Tensor Property", "Of Scalar Value", "Color Fibers By Mean Orientation", "Color Fibers By Segment Orientation", "Of Fiber Cluster Group ID" or "Solid Color".
      • Auto W/L: Adjust the window level automatically
    • Material Properties: Adjust Color, Opacity, Ambient, Diffuse, Specular, Power and Backface Culling of the displayed tracts.
      • Preview: Color preview given the adjusted properties
      • Presents: Select one of the predefined property sets


Similar Modules

  • Models

References

Information for Developers
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