UKF Tractography in Slicer 4

• 

  Projects List

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.