Difference between revisions of "UKF Tractography in Slicer 4"
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Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]] | Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]] | ||
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</gallery> | </gallery> | ||
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* Ryan Eckbo, BWH, HMS | * Ryan Eckbo, BWH, HMS | ||
* Yogesh Rathi, BWH, HMS | * Yogesh Rathi, BWH, HMS | ||
| + | * Demian Wassermann, BWH, HMS | ||
| + | * Carl-Fredrik Westin, BWH, HMS | ||
==Project Description== | ==Project Description== | ||
| Line 16: | Line 17: | ||
<h3>Objective</h3> | <h3>Objective</h3> | ||
| − | * | + | * '''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. | ||
| + | |||
| + | |||
</div> | </div> | ||
<div style="width: 27%; float: left; padding-right: 3%;"> | <div style="width: 27%; float: left; padding-right: 3%;"> | ||
<h3>Approach, Plan</h3> | <h3>Approach, Plan</h3> | ||
| − | + | ||
| − | |||
| − | |||
</div> | </div> | ||
<div style="width: 27%; float: left; padding-right: 3%;"> | <div style="width: 27%; float: left; padding-right: 3%;"> | ||
<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) |
| + | |||
| + | |||
| + | * 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 | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
| + | |||
| + | ==References== | ||
| + | Reference for 2-tensor tractography | ||
| + | # http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html | ||
| + | |||
| + | 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. | ||
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.
