Difference between revisions of "UKF Tractography in Slicer 4"
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<h3>Progress</h3> | <h3>Progress</h3> | ||
| + | * Refactored code as 3 modules (main plus 2 utility functions) bundled into an extension (as per the Slicer4 recommendation) | ||
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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 | ||
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| + | * Got CTest working for Slicer build | ||
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| + | * Created and tested the .s4ext file | ||
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| + | * Tested Superbuild, Slicer4 build, and local .s4ext build on a Mac and a Fedora Linux machine | ||
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| + | * Made new git repo and updated the documentation | ||
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| + | '''TODO''' | ||
| + | * Get CTest to work in Superbuild | ||
| + | |||
| + | * Finish running all the tests | ||
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| + | * Create logo and take snapshots | ||
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| + | * Upload .s4ext file | ||
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Reference for 1-tensor and 2-tensor + free-water | Reference for 1-tensor and 2-tensor + free-water | ||
# C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi, | # 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:
- Change and update the UKFTractography.xml file for receiving a .vtk file as output.
- Setup CTest and ensure its working.
- 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.
- Design a logo for the extension module.
- Document the module (including utility functions) -- make a wiki page. (Include the References to the appropriate papers and make nice snapshots).
- Add the 2 utility functions to the extension module and verify if they work.
- Optional:
- Use the VTK library to output the data (.vtp).
- Future Work:
- 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
Reference for 1-tensor and 2-tensor + free-water
- 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.
