Difference between revisions of "2012 Winter Project Week:EndoSeg"

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__NOTOC__
 
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<gallery>
 
<gallery>
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Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
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Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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</gallery>
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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<gallery>
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Image:CARMA_N19_Atlas_LGE.png|Atlas Image
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Image:CAMRA_N26_LGE.png|Non-atlas Image
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<gallery>
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Image:AFibEndoSegAtlasAndRSS_axial.png|Axial view of segmentation result. Red contour: manual segmentation; Green mask: automatic segmentation
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Image:AFibEndoSegAtlasAndRSS_sagittal.png|Sagittal view
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Image:AFibEndoSegAtlasAndRSS_coronal.png|Coronal view
 
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</gallery>
  
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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 Project/<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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Yi Gao, Liang-Jia Zhu, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum
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* Utah: Tom Fletcher, Ross Whitaker
 
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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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 methods for segmenting the endocardium from the DE-MRI. The current proposed method is a multi-atlas based registration approach.  The user is presented with a weighted average of all registered atlas segmentations.  The final LA segmentation is a thresholded volume from this weighted average.  Weighting is based on the accuracy of the registration, as determined by a mutual information metric.
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* There is a prototype module developed by Yi that is currently in Slicer.  We propose to expand and tweak this module to specifications determined by our experience using the algorithm on many real patient datasets.
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* We will also discuss posssible collaborative paper ideas based on this work.
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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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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* Improve the speed and accuracy using the multi-scale scheme
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* Improve the accuracy of atlas segmentation accuracy with better label fusion techniques.
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Our plan for the project week is to first try out <bar>,...
 
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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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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The current segmentation module is in the Slicer extension manager.
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This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
  
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#ITK Module
 
 
#Slicer Module
 
#Slicer Module
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##Built-in
 
 
##Extension -- commandline
 
##Extension -- commandline
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##Extension -- loadable
 
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#Other (Please specify)
 
  
 
==References==
 
==References==
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
 
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* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
 
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* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
 
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* Goodlett C, Corouge I, Jomier M, Gerig G, 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 .
 
  
 
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</div>

Latest revision as of 21:55, 12 January 2012

Home < 2012 Winter Project Week:EndoSeg

  • Atlas Image

  • Non-atlas Image

  • Axial view of segmentation result. Red contour: manual segmentation; Green mask: automatic segmentation

  • Sagittal view

  • Coronal view


Key Investigators

Yi Gao, Liang-Jia Zhu, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum

Objective

  • We are developing methods for segmenting the endocardium from the DE-MRI. The current proposed method is a multi-atlas based registration approach. The user is presented with a weighted average of all registered atlas segmentations. The final LA segmentation is a thresholded volume from this weighted average. Weighting is based on the accuracy of the registration, as determined by a mutual information metric.
  • There is a prototype module developed by Yi that is currently in Slicer. We propose to expand and tweak this module to specifications determined by our experience using the algorithm on many real patient datasets.
  • We will also discuss posssible collaborative paper ideas based on this work.

Approach, Plan

  • Improve the speed and accuracy using the multi-scale scheme
  • Improve the accuracy of atlas segmentation accuracy with better label fusion techniques.

Progress

The current segmentation module is in the Slicer extension manager.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

  1. Slicer Module
    1. Extension -- commandline

References

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