2011 Winter Project Week:GAMBITCorticalThicknessAnalysis

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Home < 2011 Winter Project Week:GAMBITCorticalThicknessAnalysis
Sulcal depth overlayed on inflated cortical surfaces

Key Investigators

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


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:

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

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)


  • 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)


  • 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