Difference between revisions of "Projects/Diffusion/2007 Project Week Slicer3 Tractography Editor"

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__NOTOC__
 
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===Key Investigators===
 
===Key Investigators===
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* BWH: Raul San Jose, Lauren O'Donnell, Alex Yarmarkovich
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* BWH: Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich
  
 
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<h1>Objective</h1>
 
<h1>Objective</h1>
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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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Initial development of tractography editing tools.  These will eventually include region of interest based selection of fiber bundles in slicer 3, conversion of fiber bundles to voxels, etc.
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
  
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
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Build on existing MRML tractography display infrastructure to allow ROI selection of fibers.
 +
 
 +
Software for the MRML infrastructure and tractography display has been implemented, and is undergoing further improvement.  Software for whole brain seeding is being developed in slicer3 as a concurrent programming week project.
 +
 
 +
Our plan for the project week is to create a CLP module to do region of interest selection of whole brain tractography.
  
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Our plan for the project week is to first try out <bar>,...
 
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
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A CLP module, Tractography->Editor->ROISelect, has been created.
  
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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Also, another CLP module for probing volumes with models ("painting" scalars on models) was created and checked into Slicer3 svn.
  
 +
There were discussions about simpler API for display of data like tractography (that needs pipeline(s) to convert to displayable polydata) with Alex, Steve, Raul, and Demian.
 +
 +
We also planned to enable future display of tractography with non-tensor or multiple tensor data attached (with Raul and Demian).
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 +
We fixed a bug with MRML scene reading for fiber bundles, so that is working correctly now.
 
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{|
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|[[Image:Photo_27.jpg|thumb|320px|Before]]
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|[[Image:Photo_28.jpg|thumb|320px|After]]
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===References===
 
===References===
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* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
 
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* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
 
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* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
 
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* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
 

Latest revision as of 14:42, 29 June 2007

Home < Projects < Diffusion < 2007 Project Week Slicer3 Tractography Editor
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Tract display in Slicer3.


Key Investigators

  • BWH: Lauren O'Donnell, Raul San Jose, Alex Yarmarkovich

Objective

Initial development of tractography editing tools. These will eventually include region of interest based selection of fiber bundles in slicer 3, conversion of fiber bundles to voxels, etc.

Approach, Plan

Build on existing MRML tractography display infrastructure to allow ROI selection of fibers.

Software for the MRML infrastructure and tractography display has been implemented, and is undergoing further improvement. Software for whole brain seeding is being developed in slicer3 as a concurrent programming week project.

Our plan for the project week is to create a CLP module to do region of interest selection of whole brain tractography.

Progress

A CLP module, Tractography->Editor->ROISelect, has been created.

Also, another CLP module for probing volumes with models ("painting" scalars on models) was created and checked into Slicer3 svn.

There were discussions about simpler API for display of data like tractography (that needs pipeline(s) to convert to displayable polydata) with Alex, Steve, Raul, and Demian.

We also planned to enable future display of tractography with non-tensor or multiple tensor data attached (with Raul and Demian).

We fixed a bug with MRML scene reading for fiber bundles, so that is working correctly now.


Before
After



References

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