Difference between revisions of "DBP2:MIND:RoadmapProject"

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(New page: {| |thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page ]] |[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through ...)
 
 
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|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
 
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
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|[[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:Lupus Demo001.png|thumb|320px|Example Results of Lesion Classification]]
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|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
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|[[Image:Lesion module.png|thumb|320px|Current Slicer3 Module]]
 
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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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*H. Jeremy Bockholt
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* Utah: Tom Fletcher, Ross Whitaker
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*Mark Scully
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*Ross Whitaker
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*Steve Pieper
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*Vincent Magnotta
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*Kilian Pohl
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*Brad Davis
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*Marcel Prastawa
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*Guido Gerig
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*Sonja Pujol
  
 
<div style="margin: 20px;">
 
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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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Finish the roadmap module, design and implement a testing strategy and work on the end-to-end tutorial for white matter lesion classification
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</div>
 
</div>
  
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
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The Slicer3 module will allow co-registration of user-selected T1, T2, and FLAIR images. The module will automatically label all brain voxels into either gray, white, csf, or lesion as tissues types. Lesions will be automatically clustered such that the anatomical location and volume can be summarized. 
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 +
Review and summarize results of each of classification approaches thus far.
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Sketch out methods paper and clinical application paper.
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Finalize content to be presented for SFN 2008 poster/presentation.
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Work with Sonja on timeline and process for creating tutorial and process for release of tool and data (SFN 2008)?
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Answer question, where do roadmap projects that share data, share it from, publication database, BIRN project, XNAT Central, other service, provide own?
  
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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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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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Plan is to release end-to-end tutorial at the 2008 Society for Neuroscience Annual meeting.
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 +
Deliverables for this week
 +
#Laid out the logic and components of the Joint Histogram matching filter for Intensity Standardization based on treating joint histograms as images and registering them to construct a deformation field.
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#Integrated visualization of ROIs that lesions impinge upon using the volume renderer and met with Wendy on integrating the output with the Query Atlas.
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#interested in working with the unbiased atlas work for lesion location (talk with sylvain)
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#Met with Killian on tuning the parametization of EM-Segment to improve our lesion classification.
 +
 +
In terms of fine tuning lesion classification:
 +
#We worked with Kilian on parameterization of EM-Segment
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#We worked with Marcel on using his method for lesion classification
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#We worked with Vince Magnotta on his method for lesion classification
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 +
Future Work:
  
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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.
 
  
 
</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 14:07, 27 June 2008

Home < DBP2:MIND:RoadmapProject
Return to Project Week Main Page
Example Results of Lesion Classification
Current Slicer3 Module




Key Investigators

  • H. Jeremy Bockholt
  • Mark Scully
  • Ross Whitaker
  • Steve Pieper
  • Vincent Magnotta
  • Kilian Pohl
  • Brad Davis
  • Marcel Prastawa
  • Guido Gerig
  • Sonja Pujol

Objective

Finish the roadmap module, design and implement a testing strategy and work on the end-to-end tutorial for white matter lesion classification

Approach, Plan

The Slicer3 module will allow co-registration of user-selected T1, T2, and FLAIR images. The module will automatically label all brain voxels into either gray, white, csf, or lesion as tissues types. Lesions will be automatically clustered such that the anatomical location and volume can be summarized.

Review and summarize results of each of classification approaches thus far.

Sketch out methods paper and clinical application paper.

Finalize content to be presented for SFN 2008 poster/presentation.

Work with Sonja on timeline and process for creating tutorial and process for release of tool and data (SFN 2008)?

Answer question, where do roadmap projects that share data, share it from, publication database, BIRN project, XNAT Central, other service, provide own?


Progress

Plan is to release end-to-end tutorial at the 2008 Society for Neuroscience Annual meeting.

Deliverables for this week

  1. Laid out the logic and components of the Joint Histogram matching filter for Intensity Standardization based on treating joint histograms as images and registering them to construct a deformation field.
  2. Integrated visualization of ROIs that lesions impinge upon using the volume renderer and met with Wendy on integrating the output with the Query Atlas.
  3. interested in working with the unbiased atlas work for lesion location (talk with sylvain)
  4. Met with Killian on tuning the parametization of EM-Segment to improve our lesion classification.

In terms of fine tuning lesion classification:

  1. We worked with Kilian on parameterization of EM-Segment
  2. We worked with Marcel on using his method for lesion classification
  3. We worked with Vince Magnotta on his method for lesion classification

Future Work:



References

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