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

From NAMIC Wiki
Jump to: navigation, search
m (Created page with '==Key Investigators== * BWH: Peter Savadjiev * Iowa: Hans Johnson * BWH: Yogesh Rathi * BWH: C-F Westin ==Project Description== <div style="margin: 20px;"> <div style="width: …')
 
 
(3 intermediate revisions by one other user not shown)
Line 1: Line 1:
 +
__NOTOC__
 
==Key Investigators==
 
==Key Investigators==
 
* BWH: Peter Savadjiev
 
* BWH: Peter Savadjiev
Line 17: Line 18:
 
<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>
−
* Create a realistic test suite based on Huntington datasets for the Matlab code.
+
* Private git repository already exists at: git@github.com:BRAINSia/CompressedSensingDWI.git
−
** [HANS - Monday] Prepare test DWI data set for preparing data
+
* Debug and test the fiberTractDispersion code
−
 
+
* Implement needed changes to the default behaviour of UKFTractography
−
* Create a VTK reader/writer in matlab, in order to the test the matlab code.
+
* Separate fiberTractDispersion from UKFTractography to create an independent Slicer extension.
−
** [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
 
−
 
 
 
</div>
 
</div>
−
</div>
+
<div style="width: 27%; float: left; padding-right: 3%;">
−
 
 
−
<div style="margin: 20px;">
 
−
<div style="width: 95%; float: left; padding-right: 3%;">
 
 
<h3>Progress</h3>
 
<h3>Progress</h3>
−
* Private git repository created at: git@github.com:BRAINSia/CompressedSensingDWI.git
+
* Worked on implementing changes to the UKFTractography extension.
−
* Spent time debugging the vtk readers/writers for MATLAB, in order to test the MATLAB code.
+
* Discovered two new issues, one involving cmake, one involving irk multithreading.
−
* Wrote XML interfaces for the fiber tract dispersion extension, and for the compressed sensing HARDI estimation.
+
* The issue with cmake should be under control.
−
[[File:DWIDispersion_xml_interfaces.png||1000px]]
+
* The issue with itk multithreading is work in progress.
−
* Next steps: continue debugging the vtk readers/writers for MATLAB, and begin translating the algorithm implementation from MATLAB to C++.
+
* Worked on debugging fibertractdispersion
 +
* Had several discussions with Hans, JC, Ron.
 
</div>
 
</div>
 
</div>
 
</div>

Latest revision as of 11:57, 30 June 2017

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

  • Worked on implementing changes to the UKFTractography extension.
  • Discovered two new issues, one involving cmake, one involving irk multithreading.
  • The issue with cmake should be under control.
  • The issue with itk multithreading is work in progress.
  • Worked on debugging fibertractdispersion
  • Had several discussions with Hans, JC, Ron.
Retrieved from "https://www.na-mic.org/w/index.php?title=2014_Summer_Project_Week:FiberTractDispersion&oldid=96955"