Difference between revisions of "UKF Tractography in Slicer 4"

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<gallery>
 
<gallery>
 
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:ScarSeg_EM.png‎| Scar tissue identification.
 
 
</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>
  
* We are developing methods for identifying scar tissue from CARMA data. Our previous method demonstrates an effective identification ability for DE-MRI data. In this method, the intensity distribution inside the LA myocardial wall is modeled as a mixture of Gaussians. To improve the performance of this method, we will integrate the intensity information from the LA chamber into the overall identification procedure.  
+
* '''High Priority''':
* We will discuss possible improvements for scar identification.  
+
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>
* Design an identification scheme using the LA intensity as a prior
+
 
* Test the method using CARMA data
 
* Deliver the implementation in CLI module.
 
 
</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:

  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.