Difference between revisions of "SkullStripper"

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(create a wiki page to describe development of Slicer3 SkullStripper module)
 
 
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==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* University of Heidelberg: Martin Loepprich MS
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* Utah: Tom Fletcher, Ross Whitaker
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* MIT CSAIL: Sylvain Jaume PhD
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* Harvard Medical School: Andriy Fedorov PhD, Ron Kikinis MD
  
 
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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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Skull Stripping is a 3D image processing technique to mask out non-brain areas in MRI images.
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Skull Stripping is often required before applying a segmentation technique such as the
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[http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segmentation].
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We are developing a Skull Stripping module in Slicer3 that will be able to work both on human MRIs and on monkey MRIs.
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This project is in collaboration with the NA-MIC project for the investigation of
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[http://wiki.na-mic.org/Wiki/index.php/Measuring_Alcohol_Stress_Interaction Alcohol Stress Interaction]
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using monkey MRI images by Andriy Fedorov (BWH), Xiaoxing Li (VT) and Chris Wyatt (VT).
  
 
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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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Our module, called SkullStripper, is based on the work of the NA-MIC consortium
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done by Snehashis Roy (JHU), Xiaodong Tao (GE) and Nicole Aucoin (BWH).
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Our plan for the project week is to first try out <bar>,...
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First we will perform a comparison study of the Slicer3 module SkullStripper
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and the FSL Brain Extraction Tool (BET).
  
 
</div>
 
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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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==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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*NA-MIC Project Week [http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping Skull Stripping] June 2009, Boston
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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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*FSL Brain Extraction Tool [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html BET]
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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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*Analysis and validation of automated skull stripping tools: A validation study based on 296 MR images from Honolulu Asia aging study, S.W. Hartley, A.I. Scher, E.S.C. Korf, L.R. White and L.J. Launer
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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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*A joint registration and segmentation approach to skull stripping, Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince ISBI 2007.
  
 
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Latest revision as of 23:25, 29 October 2009

Home < SkullStripper

  • Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.

  • Regression of FA data; solid line represents the mean and dotted lines the standard deviation.

Instructions for Use of this Template

  1. Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
  2. Copy the entire text of this page into the page created above
  3. Link the created page into the list of projects for the project event
  4. Delete this section from the created page
  5. Send an email to tkapur at bwh.harvard.edu if you are stuck

Key Investigators

  • University of Heidelberg: Martin Loepprich MS
  • MIT CSAIL: Sylvain Jaume PhD
  • Harvard Medical School: Andriy Fedorov PhD, Ron Kikinis MD

Objective

Skull Stripping is a 3D image processing technique to mask out non-brain areas in MRI images. Skull Stripping is often required before applying a segmentation technique such as the EM Segmentation. We are developing a Skull Stripping module in Slicer3 that will be able to work both on human MRIs and on monkey MRIs. This project is in collaboration with the NA-MIC project for the investigation of Alcohol Stress Interaction using monkey MRI images by Andriy Fedorov (BWH), Xiaoxing Li (VT) and Chris Wyatt (VT).

Approach, Plan

Our module, called SkullStripper, is based on the work of the NA-MIC consortium done by Snehashis Roy (JHU), Xiaodong Tao (GE) and Nicole Aucoin (BWH). First we will perform a comparison study of the Slicer3 module SkullStripper and the FSL Brain Extraction Tool (BET).

Progress


References

  • NA-MIC Project Week Skull Stripping June 2009, Boston
  • FSL Brain Extraction Tool BET
  • Analysis and validation of automated skull stripping tools: A validation study based on 296 MR images from Honolulu Asia aging study, S.W. Hartley, A.I. Scher, E.S.C. Korf, L.R. White and L.J. Launer
  • A joint registration and segmentation approach to skull stripping, Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince ISBI 2007.
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