Difference between revisions of "2014 Summer Project Week:FiberTractDispersion"

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* Create a realistic test suite based on Huntington datasets for the Matlab code.
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* Private git repository already exists at: git@github.com:BRAINSia/CompressedSensingDWI.git
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** [HANS - Monday] Prepare test DWI data set for preparing data
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* Debug and test the fiberTractDispersion code
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* Implement needed changes to the default behaviour of UKFTractography
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* Create a VTK reader/writer in matlab, in order to the test the matlab code.
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* Separate fiberTractDispersion from UKFTractography to create an independent Slicer extension.
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** [KENT -- DONE]  git@github.com:BRAINSia/CompressedSensingDWI.git
 
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** [PETER - DONE] Build github version of readers/writers
 
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** [PETER - DONE] Manually test vtk readers/writers, and convert existing test to use the binary forms
 
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* Convert the Matlab code to C++/ITK
 
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** [HANS/PETER - DONE]  Create design document (i.e. this page and paer/pencil) to describe the intended inputs and outputs.
 
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** [PETER -- DONE] - Write desired command line interface psuedocode  "caluclateDispersion --inputTract <wholebrain.vtp> --mask <roi.nrrd> --outputTract <decoratedversionofinput.vtp> "
 
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** [HANS/PETER -- DONE] - Create shell program in psydocode/comments with  XML and cxx files with description of basic IO programming needed
 
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** [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.
 
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*Create a Slicer extension
 
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Revision as of 12:38, 21 June 2014

Home < 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

  • Private git repository already exists at: git@github.com:BRAINSia/CompressedSensingDWI.git
  • Debug and test the fiberTractDispersion code
  • Implement needed changes to the default behaviour of UKFTractography
  • Separate fiberTractDispersion from UKFTractography to create an independent 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.

DWIDispersion xml interfaces.png

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