2010 WinterProject Week CorticalThicknessAnalysis - Revision history

Cvachet: /* Key Investigators */

2010-01-08T17:51:41Z

Key Investigators

Cvachet: /* Key Investigators */

2010-01-08T16:23:44Z

Key Investigators

Cvachet: /* Key Investigators */

2009-12-15T19:59:10Z

Key Investigators

Cvachet: Created page with 'NOTOC Image:PW-SLC2010.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'

2009-12-15T17:29:33Z

Created page with '__NOTOC__ <gallery> Image:PW-SLC2010.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'

New page

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
Image:BrainDevelopment.jpg|Brain development
Image:MeshBasedCortThick_CorticalThickness.jpg|Cortical thickness on white matter surface
Image:MeshBasedCortThick_SulcalDepth.jpg‎|Sucal depth on genus-zero cortical surface
Image:MeshBasedCortThick_Particles.jpg‎|Particles on inflated genus-zero cortical surface
</gallery>

==Key Investigators==
* UNC: Clement Vachet, Cedric Mathieu, Ipek Oguz, Marc Niethammer, Heather Cody Hazlett, Martin Styner
* Isomics: Steve Pieper

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<h3>Objective</h3>
We would like to create end-to-end applications within Slicer3 allowing individual and group analysis of regional (voxel-based) and local (mesh-based) cortical thickness.

Such a workflow applied to the young brain (2-4 years old) is our goal in order to start a longitudinal study of early brain development in [[DBP2:UNC|autism (UNC DBP)]].

See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.

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<h3>Approach, Plan</h3>

Our approach is described in the following wiki pages:
*[[DBP2:UNC:Regional_Cortical_Thickness_Pipeline|Voxel-based regional cortical thickness analysis]]
*[[DBP2:UNC:Local_Cortical_Thickness_Pipeline|Mesh-based local cortical thickness analysis]]

Our plan for the project week is to:

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<h3>Progress</h3>

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==References==
*I. Oguz, M. Niethammer, J. Cates, R. Whitaker, T. Fletcher, C. Vachet, and M. Styner, Cortical Correspondence with Probabilistic Fiber Connectivity, Information Processing in Medical Imaging, IPMI 2009, LNCS, in print.
*H.C. Hazlett, C. Vachet, C. Mathieu, M. Styner, J. Piven, Use of the Slicer3 Toolkit to Produce Regional Cortical Thickness Measurement of Pediatric MRI Data, presented at the 8th Annual International Meeting for Autism Research (IMFAR) Chicago, IL 2009.
*C. Mathieu, C. Vachet, H.C. Hazlett, G. Geric, J. Piven, and M. Styner, ARCTIC – Automatic Regional Cortical ThICkness Tool, UNC Radiology Research Day 2009 abstract
*C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Mesh-based Local Cortical Thickness Framework, UNC Radiology Research Day 2009 abstract

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@@ Line 49: / Line 49: @@
 ARCTIC:
 *Source code updated
-*Works again as a Slicer3 extension
+*Works again as a Slicer3 extension module

← Older revision		Revision as of 16:23, 8 January 2010
Line 42:		Line 42:
	<h3>Progress</h3>		<h3>Progress</h3>

		+	NITRC:
		+	*Elderly atlas now publicly available
		+	*MRML scenes added for each available atlas: [http://www.nitrc.org/projects/unc_brain_atlas/ human brain atlas] and [http://www.nitrc.org/projects/primate_atlas/ primate brain atlas]
		+
		+
		+	ARCTIC:
		+	*Source code updated
		+	*Works again as a Slicer3 extension
		+
		+
		+	Population analysis:
		+	*Meetings with Wendy Plesniak, Daniel Marcus, Timothy Olsen, John Paulett, Steve Pieper, Julien Jomier, Martin Styner, Corentin Hamel
		+	*Better understanding of how population analysis could be performed within Slicer3, using BatchMake and XNAT
		+
		+
		+	Mesh based cortical thickness pipeline:
		+	*Meeting with Josh Cates and Martin Styner regarding particle correspondence (usage and future options)
		+	*Applying individual pipeline to small pediatric dataset

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@@ Line 22: / Line 22: @@
 See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.
 </div>
@@ Line 38: / Line 33: @@
 *[[DBP2:UNC:Local_Cortical_Thickness_Pipeline|Mesh-based local cortical thickness analysis]]
-Our plan for the project week is to:
+Our plan for the project week is to follow-up on the local cortical thickness pipeline and apply it to a small pediatric dataset.

2010 WinterProject Week CorticalThicknessAnalysis - Revision history

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: Created page with '__NOTOC__ Image:PW-SLC2010.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'

Cvachet: Created page with 'NOTOC Image:PW-SLC2010.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'