Difference between revisions of "UKF Tractography in Slicer 4"

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<h3>Progress</h3>
 
<h3>Progress</h3>
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* Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)
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 +
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* Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt
 +
 +
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* Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with the new changes
 +
 +
 +
* Got CTest working for Slicer build
 +
 +
 +
* Created and tested the .s4ext file
 +
 +
 +
* Tested Superbuild, Slicer4 build, and local .s4ext build on a Mac and a Fedora Linux machine
 +
 +
 +
* Made new git repo and updated the documentation
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 +
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'''TODO'''
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* Get CTest to work in Superbuild
 +
 +
* Finish running all the tests
 +
 +
* Create logo and take snapshots
 +
 +
* Upload .s4ext file
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==References==
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Reference for 2-tensor tractography
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# http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html
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 +
Reference for 1-tensor and 2-tensor + free-water
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# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,
 +
"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop
 +
on computational diffusion MRI, 2012.

Latest revision as of 05:05, 11 January 2013

Home < UKF Tractography in Slicer 4

Key Investigators

  • Ryan Eckbo, BWH, HMS
  • Yogesh Rathi, BWH, HMS
  • Demian Wassermann, BWH, HMS
  • Carl-Fredrik Westin, BWH, HMS

Project Description

Objective

  • High Priority:

Have a working UKFtractography module in Slicer4 extension:

  1. Change and update the UKFTractography.xml file for receiving a .vtk file as output.
  2. Setup CTest and ensure its working.
  3. Verify that the Tractography module works on a test invivo data set
    • Verify that the following 4 models work properly. 1-Tensor, 1-Tensor with Free-water, 2-tensor, 2-tensor with free-water.
  4. Design a logo for the extension module.
  5. Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
  6. Add the 2 utility functions to the extension module and verify if they work.
  • Optional:
  1. Use the VTK library to output the data (.vtp).
  • Future Work:
  1. Move from boost to ITK multithreading.


Approach, Plan

Progress

  • Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation)


  • Updated the 3 module CMakeLists.txt to use the latest macros (e.g. SEMMacroBuildCLI) and added an extension specific CMakeLists.txt


  • Updated, fixed, and tested the Superbuild CMakelists.txt to be compatible with the new changes


  • Got CTest working for Slicer build


  • Created and tested the .s4ext file


  • Tested Superbuild, Slicer4 build, and local .s4ext build on a Mac and a Fedora Linux machine


  • Made new git repo and updated the documentation


TODO

  • Get CTest to work in Superbuild
  • Finish running all the tests
  • Create logo and take snapshots
  • Upload .s4ext file

References

Reference for 2-tensor tractography

  1. http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html

Reference for 1-tensor and 2-tensor + free-water

  1. C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,

"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop on computational diffusion MRI, 2012.

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