Difference between revisions of "2008 Summer Project Week:DWI-DTI PrepTools"

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__NOTOC__
 
__NOTOC__
  
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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 NA-MIC/Projects/Theme-Name/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===
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* UNC: Heather Cody Hazlett, Martin Styner, Zhexing Liu
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* Utah: Tom Fletcher, Ross Whitaker
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* Utah: Casey Goodlett, Guido Gerig, Tom Fletcher
  
  
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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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We are developing a tool for preparing diffusion weighted and diffusion tensor image data.
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Details of the tool functionality were discussed [[2008_Core_1_UNC_Utah_DTI|between UNC and Utah]]:
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* "Protocol" based execution
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** Parameter files contain all settings
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* Handles conversion of DICOM data to volumetric formats (NRRD)
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* Automated quality control, corrects/rejects, provides reporting facility.
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* Motion correction
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* Eddy current correction
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* Interpolation of data
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* Rejection of interslice brightness
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* Local plausibility check with reconstructed DTI
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* FA/MD histogram comparison with atlas
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* Local dot product of principal direction with atlas
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* Full brain tracking for flips/permutations of axes
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* Focus QC on white matter only
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* DTI data, as well as FA/MD
  
  
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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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The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI. This tool will handle the conversion of DICOM data to volumetric image formats (NRRD), perform automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.  
  
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Our plan for the project week is to first try out <bar>,...
 
 
</div>
 
</div>
  
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<h1>Progress</h1>
 
<h1>Progress</h1>
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During the 2008 project week:
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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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* We met with Xiaodong Tao and talked with him the Dicom to nrrd transform and DTI estimation. We will incorporate his Dicom/nrrd format transform work into our pipeline.
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* We met with Casey Goodlett and learned atlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on a DTI atlas.
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* We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction procedure, for some of the inferior and superior slices may contain only pieces of brain structures due to the transform during correction.
  
 
</div>
 
</div>
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</div>
 
</div>
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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 14:02, 27 June 2008

Home < 2008 Summer Project Week:DWI-DTI PrepTools
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Key Investigators

  • UNC: Heather Cody Hazlett, Martin Styner, Zhexing Liu
  • Utah: Casey Goodlett, Guido Gerig, Tom Fletcher


Objective

We are developing a tool for preparing diffusion weighted and diffusion tensor image data.

Details of the tool functionality were discussed between UNC and Utah:

  • "Protocol" based execution
    • Parameter files contain all settings
  • Handles conversion of DICOM data to volumetric formats (NRRD)
  • Automated quality control, corrects/rejects, provides reporting facility.
  • Motion correction
  • Eddy current correction
  • Interpolation of data
  • Rejection of interslice brightness
  • Local plausibility check with reconstructed DTI
  • FA/MD histogram comparison with atlas
  • Local dot product of principal direction with atlas
  • Full brain tracking for flips/permutations of axes
  • Focus QC on white matter only
  • DTI data, as well as FA/MD


Approach, Plan

The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI. This tool will handle the conversion of DICOM data to volumetric image formats (NRRD), perform automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.

Progress

During the 2008 project week:

  • We met with Xiaodong Tao and talked with him the Dicom to nrrd transform and DTI estimation. We will incorporate his Dicom/nrrd format transform work into our pipeline.
  • We met with Casey Goodlett and learned atlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on a DTI atlas.
  • We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction procedure, for some of the inferior and superior slices may contain only pieces of brain structures due to the transform during correction.


References

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