Difference between revisions of "Collaboration/Harvard IIC/AstroMed"

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{|
 
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|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
 
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
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|[[Image:Future-astromed-slicer-mockup.png|thumb|320px|Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
 
 
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__NOTOC__
 
__NOTOC__
 
===Key Investigators===
 
===Key Investigators===
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* Mike Halle: BWH/Harvard IIC
* Utah: Tom Fletcher, Ross Whitaker
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* Douglas Alan: Havard IIC
 
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* Jim Miller: GE
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h1>Objective</h1>
 
<h1>Objective</h1>
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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We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now. In order to accomplish this, we need to adapt ITK and Slicer to work with astronomical world coordinate systems.
 
 
 
 
 
</div>
 
</div>
  
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
  
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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Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site].  The main challenge to this approach is currently the impedance mismatch between celestial coordinates and medical imaging coordinates.
  
Our plan for the project week is to first try out <bar>,...
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Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary.  If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.
 
</div>
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
  
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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We have implemented a FITS reader for ITK.  (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.
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TODO: More stuff here.
  
 
</div>
 
</div>
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===References===
 
===References===
 +
 +
TODO: Replace the following with our papers.
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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.
 
* 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.
 
* 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.
 
* 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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=Additional Information=
 
=Additional Information=
Please link to pages with additional information here.
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* [http://astromed.iic.harvard.edu Astronomical Medicine web site]

Revision as of 16:40, 21 June 2007

Home < Collaboration < Harvard IIC < AstroMed
Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.


Key Investigators

  • Mike Halle: BWH/Harvard IIC
  • Douglas Alan: Havard IIC
  • Jim Miller: GE

Objective

We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now. In order to accomplish this, we need to adapt ITK and Slicer to work with astronomical world coordinate systems.

Approach, Plan

Our approach is summarized on the Astronomical Medicine web site. The main challenge to this approach is currently the impedance mismatch between celestial coordinates and medical imaging coordinates.

Our plan for the project week is to implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.

Progress

We have implemented a FITS reader for ITK. (FITS is the standard file format for astronomical images.) We currently use this reader to convert FITS files into NRRD files so that they can be read into Slicer.

TODO: More stuff here.



References

TODO: Replace the following with our papers.

  • 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.
  • 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.
  • 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
  • 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 .

Additional Information