2011 Winter Project Week:GAMBITCorticalThicknessAnalysis - Revision history

Cvachet at 17:35, 14 January 2011

2011-01-14T17:35:39Z

Cvachet: /* Key Investigators */

2011-01-14T17:19:02Z

Key Investigators

Cvachet: /* Key Investigators */

2011-01-14T15:46:47Z

Key Investigators

Cvachet at 15:46, 14 January 2011

2011-01-14T15:46:23Z

Cvachet at 20:58, 13 December 2010

2010-12-13T20:58:10Z

Cvachet at 20:39, 13 December 2010

2010-12-13T20:39:19Z

Cvachet: /* Key Investigators */

2010-12-13T19:29:07Z

Key Investigators

Cvachet: /* Key Investigators */

2010-12-13T19:25:24Z

Key Investigators

Cvachet: Created page with 'NOTOC Image:PW-SLC2011.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'

2010-12-13T19:21:17Z

Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'

New page

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
Image:BrainDevelopment.jpg|[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness]
Image:MeshBasedCortThick_Particles.jpg‎|Particles on inflated genus-zero cortical surface
</gallery>
{|
| [[Image:GAMBIT_QC_CorticalThickness.png|thumb|500px|Cortical thickness overlayed on inflated cortical surfaces]]
| [[Image:GAMBIT_QC_SulcalDepth.png|thumb|500px|Sulcal depth overlayed on inflated cortical surfaces]]
|}

==Key Investigators==
* UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner

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

<h3>Objective</h3>
We would like to create end-to-end applications within Slicer3 allowing voxel-based and mesh-based group analyses of 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.

</div>

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

<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]]

Two 3D Slicer high-level modules -directly available as extensions- have been developped in that regard:
*[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
*[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness ]

Our plan for the project week is to:
* Improve GAMBIT overall distribution:
** Include/Improve download/compilation of external packages
** Improve ShapeWorks integration within Slicer3 (meeting with SCI members)

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:

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

==References==
*C. Vachet, H. Cody Hazlett, M. Niethammer, I. Oguz, J. Cates, R. Whitaker, J. Piven, M. Styner, Group-wise Automatic Mesh-Based Analysis of Cortical Thickness, accepted to SPIE 2011
*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. 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 2010 abstract
*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
*J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. Shape Modeling and Analysis with Entropy-Based Particle Systems. Information Processing in Medical Imaging IPMI 2007, LNCS 4584, pp. 333-345, 2007

</div>

@@ Line 54: / Line 54: @@
 *Attended the Particle Shape Correspondence Breakout
-** ShapeWorks will be available soon on NITRC and integrated within 3D Slicer as an extension
+** ShapeWorks will be available soon as a SVN repository on NITRC (from CVS on GForge) and directly integrated within 3D Slicer as an extension
 *GAMBIT now includes download/compilation of external packages: ABC, ShapeWorks, BRAINSFit, BRAINSResample, BRAINSDemonWarp...

@@ Line 55: / Line 55: @@
 *Attended the Particle Shape Correspondence Breakout
 ** ShapeWorks will be available soon on NITRC and integrated within 3D Slicer as an extension
-*GAMBIT now includes download/compilation of external packages:
+*GAMBIT now includes download/compilation of external packages: ABC, ShapeWorks, BRAINSFit, BRAINSResample, BRAINSDemonWarp...
 </div>

@@ Line 53: / Line 53: @@
 <h3>Progress</h3>
+*Attended the Particle Shape Correspondence Breakout
 </div>

@@ Line 44: / Line 44: @@
 Our plan for the project week is to improve GAMBIT's overall distribution:
-** Include/Improve download/compilation of external packages
+*Include/Improve download/compilation of external packages
-** Improve ShapeWorks integration within Slicer3 (meeting with SCI members)
+*Improve ShapeWorks integration within Slicer3 (meeting with SCI members)
 </div>

@@ Line 7: / Line 7: @@
 </gallery>
 {|
 | [[Image:GAMBIT_QC_SulcalDepth.png|thumb|500px|Sulcal depth overlayed on inflated cortical surfaces]]
 |}

@@ Line 4: / Line 4: @@
 Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
 Image:GAMBITLogo.png|[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness]
-Image:MeshBasedCortThick_Particles.jpg‎|Particles on inflated genus-zero cortical surface
+Image:BrainDevelopment.jpg|Brain development
 </gallery>
 {|

2011 Winter Project Week:GAMBITCorticalThicknessAnalysis - Revision history

Cvachet at 17:35, 14 January 2011

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet at 15:46, 14 January 2011

Cvachet at 20:58, 13 December 2010

Cvachet at 20:39, 13 December 2010

Cvachet: /* Key Investigators */

Cvachet: /* Key Investigators */

Cvachet: Created page with '__NOTOC__ Image:PW-SLC2011.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'

Cvachet: Created page with 'NOTOC Image:PW-SLC2011.png|Projects List Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regi…'