View source for UKF Tractography in Slicer 4

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Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
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==Key Investigators==

* Ryan Eckbo, BWH, HMS
* Yogesh Rathi, BWH, HMS
* Demian Wassermann, BWH, HMS
* Carl-Fredrik Westin, BWH, HMS

==Project Description==

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<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.



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<h3>Approach, Plan</h3>

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<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

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==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.