SkullStripper - Revision history

Sylvainjaume: /* References */

2009-10-29T23:25:10Z

References

Sylvainjaume: /* Key Investigators */

2009-10-29T23:16:23Z

Key Investigators

Sylvainjaume: create a wiki page to describe development of Slicer3 SkullStripper module

2009-10-29T22:08:42Z

create a wiki page to describe development of Slicer3 SkullStripper module

New page

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

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

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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<h3>Objective</h3>
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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<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
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==
*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.
* 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.
* 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.
* 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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@@ Line 14: / Line 14: @@
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* University of Heidelberg: Martin Loepprich MS
-* Utah: Tom Fletcher, Ross Whitaker
+* MIT CSAIL: Sylvain Jaume PhD
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@@ Line 21: / Line 22: @@
 <h3>Objective</h3>
-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.
+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
+[http://wiki.na-mic.org/Wiki/index.php/EMSegment 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
+[http://wiki.na-mic.org/Wiki/index.php/Measuring_Alcohol_Stress_Interaction Alcohol Stress Interaction]
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@@ Line 34: / Line 36: @@
 <h3>Approach, Plan</h3>
-Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
+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).
-Our plan for the project week is to first try out <bar>,...
+First we will perform a comparison study of the Slicer3 module SkullStripper
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@@ Line 43: / Line 46: @@
 <h3>Progress</h3>

@@ Line 54: / Line 54: @@
 ==References==
-*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.
+*NA-MIC Project Week [http://wiki.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping Skull Stripping] June 2009, Boston
-* 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.
+*FSL Brain Extraction Tool [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html BET]
-* 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.
+*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
-* 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 .
+*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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