Difference between revisions of "UKF Tractography in Slicer 4"

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<h3>Objective</h3>
 
<h3>Objective</h3>
  
−
* To convert Dr. Rathi's UKF tractography Slicer3 module to a Slicer4 extension
+
* '''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.
  
−
* **High Priority**:
+
* '''Optional''':
 +
# Use the VTK library to output the data (.vtp).
  
−
  Have a working UKFtractography module in Slicer4 extension:
+
* '''Future Work''':
−
 
+
# Move from boost to ITK multithreading.
−
  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
 
−
      a). 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.
 
  
  
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<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:

  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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