2012 Winter Project Week:EndoSeg - Revision history

Ygao at 21:55, 12 January 2012

2012-01-12T21:55:09Z

Ygao at 21:54, 12 January 2012

2012-01-12T21:54:49Z

Ygao at 21:53, 12 January 2012

2012-01-12T21:53:11Z

Ygao: /* Key Investigators */

2012-01-09T20:16:23Z

Key Investigators

Cates at 22:48, 6 January 2012

2012-01-06T22:48:46Z

Cates at 20:59, 10 November 2011

2011-11-10T20:59:51Z

Ggardner at 19:41, 9 November 2011

2011-11-09T19:41:38Z

Ygao at 16:07, 9 November 2011

2011-11-09T16:07:52Z

Ygao: Created page with 'NOTOC Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

2011-11-09T15:57:43Z

Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

New page

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_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

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<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.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<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.

</div>
</div>

<div style="width: 97%; float: left;">

==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)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==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 .

</div>

@@ Line 6: / Line 6: @@
 <gallery>
 Image:CARMA_N19_Atlas_LGE.png|Atlas Image
-Image:CAMRA_N26_LGE.png|thumb|Non-atlas Image
+Image:CAMRA_N26_LGE.png|Non-atlas Image
 </gallery>

@@ Line 5: / Line 5: @@
 <gallery>
-Image:CARMA_N19_Atlas_LGE.png|thumb|left|Atlas Image
+Image:CARMA_N19_Atlas_LGE.png|Atlas Image
-Image:CAMRA_N26_LGE.png|thumb|left|Non-atlas Image
+Image:CAMRA_N26_LGE.png|thumb|Non-atlas Image
 </gallery>
 <gallery>
-Image:AFibEndoSegAtlasAndRSS_axial.png
+Image:AFibEndoSegAtlasAndRSS_axial.png|Axial view of segmentation result. Red contour: manual segmentation; Green mask: automatic segmentation
-Image:AFibEndoSegAtlasAndRSS_sagittal.png
+Image:AFibEndoSegAtlasAndRSS_sagittal.png|Sagittal view
-Image:AFibEndoSegAtlasAndRSS_coronal.png
+Image:AFibEndoSegAtlasAndRSS_coronal.png|Coronal view
 </gallery>

@@ Line 23: / Line 23: @@
 <h3>Approach, Plan</h3>
-Approach to be filled here.
+* Improve the speed and accuracy using the multi-scale scheme
 </div>

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
+Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
 </gallery>
 ==Key Investigators==
-Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum
+Yi Gao, Liang-Jia Zhu, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum
 <div style="margin: 20px;">
@@ Line 11: / Line 11: @@
 <h3>Objective</h3>
-We are developing methods for segmenting the endocardium from the DE-MRI.
+* 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.
 </div>

@@ Line 5: / Line 5: @@
 ==Key Investigators==
-Yi Gao, Liang-Jia Zhu, Josh Cates, Gregory Phillip Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum
+Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum
 <div style="margin: 20px;">

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
 </gallery>
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+Yi Gao, Liang-Jia Zhu, Josh Cates, Gregory Phillip Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum
 <div style="margin: 20px;">
@@ Line 21: / Line 11: @@
 <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.
+We are developing methods for segmenting the endocardium from the DE-MRI.
@@ Line 34: / Line 20: @@
 <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>.
+Approach to be filled here.
 </div>
@@ Line 43: / Line 27: @@
 <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.
+The current segmentation module is in the Slicer extension manager.
 </div>
@@ Line 55: / Line 38: @@
 This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 #Slicer Module
 ##Extension -- commandline
 ==References==
 </div>