2011 Winter Project Week:GAMBITCorticalThicknessAnalysis

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  Projects List

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  ARCTIC: Automatic Regional Cortical ThICkness

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  GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness

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  Brain development

Sulcal depth overlayed on inflated cortical surfaces

Key Investigators

• UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner

Objective

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 autism (UNC DBP).

See our Roadmap for more details.

Approach, Plan

Our approach is described in the following wiki pages:

• Voxel-based regional cortical thickness analysis
• Mesh-based local cortical thickness analysis

Two 3D Slicer high-level modules -directly available as extensions- have been developped in that regard:

• ARCTIC: Automatic Regional Cortical ThICkness
• GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness

Our plan for the project week is to improve GAMBIT's overall distribution:

• Include/Improve download/compilation of external packages
• Improve ShapeWorks integration within Slicer3 (meeting with SCI members)

Progress

• Attended the Particle Shape Correspondence Breakout
  • 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...

Delivery Mechanism

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

1. ITK Module
2. Slicer Module
   1. Built-in
   2. Extension -- commandline - YES
   3. Extension -- loadable
3. 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