2012 Summer Project Week:ANTS Registation - Revision history

Dmwelch: /* References */ Added Insight Journal reference

2012-05-22T20:40:07Z

References: Added Insight Journal reference

Dmwelch: Added some references and collaborators who won't be at Project week

2012-05-22T20:16:32Z

Added some references and collaborators who won't be at Project week

Dmwelch: /* Key Investigators */ Updated from template

2012-05-22T20:10:36Z

Key Investigators: Updated from template

Dmwelch: /* Instructions for Use of this Template */

2012-05-22T20:05:44Z

Instructions for Use of this Template

Dmwelch: Added ANTS webpage and image

2012-05-22T20:04:42Z

Added ANTS webpage and image

Dmwelch: Template

2012-05-14T21:21:38Z

Template

New page

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_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 2012_Winter_Project_Week:<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 44: / Line 44: @@
 ==References==
-* [http://www.picsl.upenn.edu/ANTS/ ANTS webpage: http://www.picsl.upenn.edu/ANTS/]
+* ANTS webpage: http://www.picsl.upenn.edu/ANTS/ [http://www.picsl.upenn.edu/ANTS/]
 * Avants B, Tustison N, and Song G, ANTS: Open-Source Tools for Normalization And Neuroanatomy, IEEE Transactions on Medical Imaging, pp. 1-11.
 * Avants B B, Tustison N T, Song G, Cook P A, Klein A, and Gee J C, A reproducible evaluation of ANTs similarity metric performance in brain image registration., NeuroImage, vol. 54, no. 3, pp. 2033-44, Feb. 2011.

@@ Line 7: / Line 7: @@
 ==Key Investigators==
 * Iowa: Dave Welch, Hans Johnson
-* Penn State: Brian Avants, Nick Tustison
+* Penn State: Brian Avants, Gang Song, Nick Tustison
 <div style="margin: 20px;">
@@ Line 36: / Line 36: @@
 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 -- commandline YES
 ##Extension -- loadable
 #Other (Please specify)
@@ Line 45: / Line 45: @@
 ==References==
 * [http://www.picsl.upenn.edu/ANTS/ ANTS webpage: http://www.picsl.upenn.edu/ANTS/]
-* 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.
+* Avants B, Tustison N, and Song G, ANTS: Open-Source Tools for Normalization And Neuroanatomy, IEEE Transactions on Medical Imaging, pp. 1-11.
-* 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.
+* Avants B B, Tustison N T, Song G, Cook P A, Klein A, and Gee J C, A reproducible evaluation of ANTs similarity metric performance in brain image registration., NeuroImage, vol. 54, no. 3, pp. 2033-44, Feb. 2011.

@@ Line 6: / Line 6: @@
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* Iowa: Dave Welch, Hans Johnson
-* Utah: Tom Fletcher, Ross Whitaker
+* Penn State: Brian Avants, Nick Tustison
 <div style="margin: 20px;">
@@ Line 13: / Line 13: @@
 <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 an ANTS-based registration module.
 </div>
@@ Line 26: / Line 21: @@
 <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 approach for implementing ANTS registration will be to create a command line module and integrate ANTS into the Slicer build process, if possible.
 </div>
@@ Line 35: / Line 28: @@
 <h3>Progress</h3>
 </div>
 </div>
 ==Delivery Mechanism==

@@ Line 4: / Line 4: @@
 Image:ANTSLargeDef.jpg|ANTS Brain registration to population-based template
 </gallery>
 ==Key Investigators==

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2012.png|[[2012_Summer_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:ANTSLargeDef.jpg|ANTS Brain registration to population-based template
 </gallery>
@@ Line 63: / Line 62: @@
 ==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.
+* [http://www.picsl.upenn.edu/ANTS/ ANTS webpage: http://www.picsl.upenn.edu/ANTS/]
 * 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.