Difference between revisions of "2010 Winter Project Week WM ATLAS"

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==Key Investigators==
 
==Key Investigators==
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* Lauren O'Donnell (Instructor, Harvard Medical School (BWH))
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* Lauren O'Donnell (Harvard Medical School (BWH))
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* Luis Ibanez (Kitware Inc)
 
* Carl-Fredrik Westin (Professor, Harvard Medical School (BWH) )
 
* Carl-Fredrik Westin (Professor, Harvard Medical School (BWH) )
 
* William Wells (Professor, Harvard Medical School (BWH) )
 
* William Wells (Professor, Harvard Medical School (BWH) )
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* Preprocessing
 
* Preprocessing
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** initial implementation of BatchMake modules for tensor calc, but found ipython is preferable for overall pipeline
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** Debugging of ITK congealing with Luis.
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** tested congealing implementation in ITK from NAMIC SandBox to replace our current use of original code by Lilla Zollei
 
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*** unable to output mean images due to code crash
 
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** discussions with Sandy, Lilla indicate ITK congealing broke with new ITK version, unclear when this was
 
 
** implementation of initial seeding pipeline script in ipython
 
** implementation of initial seeding pipeline script in ipython
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*** current pipeline uses slicer command line modules that call teem/vtk
 
 
** Gordon has implemented tractography methods and some probing capability in teem, may allow more direct teem/itk/vtk dependencies
 
** Gordon has implemented tractography methods and some probing capability in teem, may allow more direct teem/itk/vtk dependencies
 
* Clustering
 
* Clustering
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** looking into available packages in python
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** initial single-subject cluster test implemented in python
 
* IGT fMRI+DTI atlas
 
* IGT fMRI+DTI atlas
 
** Initial methods development: fiber-fMRI distance model (MICCAI Diffusion workshop 2009)
 
** Initial methods development: fiber-fMRI distance model (MICCAI Diffusion workshop 2009)
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** Output of matlab-generated tract predictions to slicer3
 
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Revision as of 20:51, 7 January 2010

Home < 2010 Winter Project Week WM ATLAS

  • Input from example subject: Automatically segmented fiber tracts and fMRI peak locations.

  • Output: Search region for arcuate based on fMRI locations. Yellow region is prediction of arcuate location in this patient.

Key Investigators

  • Lauren O'Donnell (Harvard Medical School (BWH))
  • Luis Ibanez (Kitware Inc)
  • Carl-Fredrik Westin (Professor, Harvard Medical School (BWH) )
  • William Wells (Professor, Harvard Medical School (BWH) )
  • Alexandra J Golby (Professor of Neurosurgery, Harvard Medical School (BWH) )
  • Gordon L. Kindlmann (Professor University of Chicago) (teem help/docs/implementation)
  • James Malcolm and Yogesh Rathi (2-tensor tractography)
  • Steve Pieper (advice on ipython and module implementation)

Objective

Eventual goal: Implement slicer module for neurosurgical planning using novel fMRI+DTI atlas.

Intermediate goals: Investigate re-implementation of tract-based morphometry pipeline in 3D Slicer, including clustering for atlas creation, atlas-based WM (white matter) segmentation and whole-brain WM coordinate system generation. Investigate integration of FMRI+DTI into atlas pipeline, for neurosurgical planning applications.

Approach, Plan

The original WM atlas pipeline consists of (over a group):

  • Preprocessing
    • DTI and FA image calculation (slicer)
    • congealing registration of FA images (Lilla's code)
    • whole-brain tract seeding (slicer2)
    • application of registration to tractography (matlab)
    • measurement of fiber-fMRI model (slicer2/matlab)
  • Atlas generation (matlab)
    • clustering of (sample from) whole-brain tractography in group
    • expert labeling of clusters to give anatomical structures
    • the above produces an atlas that can be used to segment
  • WM tract segmentation (matlab)
    • based on atlas, plus fMRI in future for IGT
  • analysis of segmented WM (matlab)
    • optimal generation of tract-based coordinate systems per anatomical structure
    • export of cluster/structure based measurements (FA, etc)
    • some statistical analysis

We propose re-implementation of much of the above in python and/or Slicer3 framework. This will enable use of the pipeline by others and our investigation of DTI+fMRI atlases for neurosurgery.

Progress

Our current goal is to decide what dependencies the atlas creation software should have and whether re-implementation in python is feasible.

  • Preprocessing
    • Debugging of ITK congealing with Luis.
    • implementation of initial seeding pipeline script in ipython
    • Gordon has implemented tractography methods and some probing capability in teem, may allow more direct teem/itk/vtk dependencies
  • Clustering
    • initial single-subject cluster test implemented in python
  • IGT fMRI+DTI atlas
    • Initial methods development: fiber-fMRI distance model (MICCAI Diffusion workshop 2009)
    • Output of matlab-generated tract predictions to slicer3

References

This work is based on the papers

Defining Spatial Relationships Between fMRI and DTI Fiber Tracts Lauren J. O'Donnell, Laura E. Rigolo, Isaiah Norton, Carl-Fredrik Westin, and Alexandra J. Golby. MICCAI Workshop on Diffusion Modeling and the Fibre Cup, 2009

Tract-Based Morphometry for White Matter Group Analysis. Lauren J. O'Donnell, Carl-Fredrik Westin, and Alexandra J. Golby. NeuroImage 45(3):832-844, 2009

Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas. Lauren O'Donnell and Carl-Fredrik Westin. IEEE Transactions in Medical Imaging 26(11):1562-1575, 2007

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