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

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

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

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

1. Got CTest working for Slicer build

1. Created and tested the .s4ext file

1. Tested Superbuild, Slicer4 build, and local .s4ext build on Mac and Fedora Linux machines

1. Made new git repo and updated the documentation

TODO

1. Get CTest to work in Superbuild

1. Finish running all the tests

1. Finish documentation, create logo, and take snapshots

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.