Difference between revisions of "2013 Summer Project Week:TractAtlasCluster"

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Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:Clusters.png|Tract clusters in a healthy control brain.
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:Clusters_points.png|Clusters across subjects, relative to landmarks from fMRI.
 
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==Instructions for Use of this Template==
 
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#Please create a new wiki page with an appropriate title for your project using the convention 2013_Summer_Project_Week:<Project Name>
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
 
* BWH: Lauren O'Donnell
 
* BWH: Lauren O'Donnell
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* Utah: Tom Fletcher, Ross Whitaker
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* Slicer gurus: thanks Steve Pieper
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* Open source/python/vtk gurus: thanks Bill Lorensen
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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The goal is to work on Slicer integration and user packaging for Python tract atlasing and clustering code.
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The goal is to work on Slicer integration and user packaging to enable open-source release of Python tract atlasing and clustering code.
  
  
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Our python package includes code implementing tract clustering, atlas labeling, registration, and fMRI-DTI modeling as part of the atlas. References are below.
 
Our python package includes code implementing tract clustering, atlas labeling, registration, and fMRI-DTI modeling as part of the atlas. References are below.
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Our plan for the project week is to focus on Slicer compatibility and user accessibility of the code.
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Our plan for the project week is to focus on Slicer compatibility and user accessibility/cleanup/documentation of the code.
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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Provided source code to collaborators in Toronto, and code was installed and tested successfully at their lab. New test scripts were written. Code was updated and initially tested to work with vtk6. For possible ease of distribution, code was tested against a new install of Canopy (new Enthought python) distribution (that includes scipy) with their provided vtk package. However that vtk package lacked some vtkCellArray wrappings needed by our code (that are present when compiling and wrapping vtk from source). A bug report was filed with Enthought regarding the wrappings, and a discussion with Bill Lorensen indicated it is due to an older version of vtk distributed with Canopy. Enthought has now told us they will update their vtk package to a more recent vtk5. Other progress: Discussions with Steve Pieper about likely/planned python packages in slicer.
  
 
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##Extension -- commandline
 
##Extension -- commandline
 
##Extension -- loadable
 
##Extension -- loadable
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#Other (Please specify)
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#Other (Please specify) YES: eventual plan is an extension but depends on packages not yet in Slicer python.
  
 
==References==
 
==References==
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* Fiber clustering versus the parcellation-based connectome
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LJ O’Donnell, AJ Golby, CF Westin
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NeuroImage 2013
 
* Unbiased Groupwise Registration of White Matter Tractography
 
* Unbiased Groupwise Registration of White Matter Tractography
 
LJ O’Donnell, WM Wells III, AJ Golby, CF Westin
 
LJ O’Donnell, WM Wells III, AJ Golby, CF Westin

Latest revision as of 14:12, 21 June 2013

Home < 2013 Summer Project Week:TractAtlasCluster

  • Tract clusters in a healthy control brain.

  • Clusters across subjects, relative to landmarks from fMRI.

Key Investigators

  • BWH: Lauren O'Donnell
  • Slicer gurus: thanks Steve Pieper
  • Open source/python/vtk gurus: thanks Bill Lorensen

Objective

The goal is to work on Slicer integration and user packaging to enable open-source release of Python tract atlasing and clustering code.


Approach, Plan

Our python package includes code implementing tract clustering, atlas labeling, registration, and fMRI-DTI modeling as part of the atlas. References are below. Our plan for the project week is to focus on Slicer compatibility and user accessibility/cleanup/documentation of the code.

Progress

Provided source code to collaborators in Toronto, and code was installed and tested successfully at their lab. New test scripts were written. Code was updated and initially tested to work with vtk6. For possible ease of distribution, code was tested against a new install of Canopy (new Enthought python) distribution (that includes scipy) with their provided vtk package. However that vtk package lacked some vtkCellArray wrappings needed by our code (that are present when compiling and wrapping vtk from source). A bug report was filed with Enthought regarding the wrappings, and a discussion with Bill Lorensen indicated it is due to an older version of vtk distributed with Canopy. Enthought has now told us they will update their vtk package to a more recent vtk5. Other progress: Discussions with Steve Pieper about likely/planned python packages in slicer.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

  1. ITK Module
  2. Slicer Module
    1. Built-in
    2. Extension -- commandline
    3. Extension -- loadable
  3. Other (Please specify) YES: eventual plan is an extension but depends on packages not yet in Slicer python.

References

  • Fiber clustering versus the parcellation-based connectome

LJ O’Donnell, AJ Golby, CF Westin NeuroImage 2013

  • Unbiased Groupwise Registration of White Matter Tractography

LJ O’Donnell, WM Wells III, AJ Golby, CF Westin Medical Image Computing and Computer-Assisted Intervention–MICCAI 2012, 123-130

  • fMRI-DTI modeling via landmark distance atlases for prediction and detection of fiber tracts

LJ O'Donnell, L Rigolo, I Norton, WM Wells III, CF Westin, AJ Golby NeuroImage 60 (1), 456-70

  • Automatic tractography segmentation using a high-dimensional white matter atlas

LJ O'Donnell, CF Westin Medical Imaging, IEEE Transactions on 26 (11), 1562-1575

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