2014 Summer Project Week:FiberTractDispersion

Key Investigators

• BWH: Peter Savadjiev
• Iowa: Hans Johnson
• BWH: Yogesh Rathi
• BWH: C-F Westin

Project Description

Objective

The fiber tract dispersion computation method of Savadjiev et al. (MICCAI 2012) has recently been converted from an implementation in Matlab to C++/ITK. However, more work needs to be done in debugging and testing the C++ implementation. Currently this method is bundled with the UKF Tractography extension, but the long term goal is to make it into a stand-alone extension.

In addition, some more debugging and testing of the UKF Tractography extension is needed.

Approach, Plan

• Create a realistic test suite based on Huntington datasets for the Matlab code.
  • [HANS - Monday] Prepare test DWI data set for preparing data

• Create a VTK reader/writer in matlab, in order to the test the matlab code.
  • [KENT -- DONE] git@github.com:BRAINSia/CompressedSensingDWI.git
  • [PETER - DONE] Build github version of readers/writers
  • [PETER - DONE] Manually test vtk readers/writers, and convert existing test to use the binary forms

• Convert the Matlab code to C++/ITK
  • [HANS/PETER - DONE] Create design document (i.e. this page and paer/pencil) to describe the intended inputs and outputs.
  • [PETER -- DONE] - Write desired command line interface psuedocode "caluclateDispersion --inputTract <wholebrain.vtp> --mask <roi.nrrd> --outputTract <decoratedversionofinput.vtp> "
  • [HANS/PETER -- DONE] - Create shell program in psydocode/comments with XML and cxx files with description of basic IO programming needed
  • [KENT -- Tuesday/Wednesday] -- Fill in I/O portions of psuedocode and make a compilable application that reads the inputTract, breaks it apart into necessary algorithmic components, and writes out the outputTract.

• Create a Slicer extension

Progress

• Private git repository created at: git@github.com:BRAINSia/CompressedSensingDWI.git
• Spent time debugging the vtk readers/writers for MATLAB, in order to test the MATLAB code.
• Wrote XML interfaces for the fiber tract dispersion extension, and for the compressed sensing HARDI estimation.

• Next steps: continue debugging the vtk readers/writers for MATLAB, and begin translating the algorithm implementation from MATLAB to C++.