2010 Summer Project Week Cortical Thickness Analysis

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Cortical thickness overlayed on inflated cortical surfaces
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 have been developped in that regard:

Our plan for the project week is to:

  • Follow-up on ARCTIC: Make it directly available as a 3D Slicer extension on MAC (compilation issues apparently)
  • Follow-up on GAMBIT: further developmenent
    • Prodiving new 3D Slicer MRML scenes for improved quality control
    • Meet with Manasi Datar and Josh Cates (Utah U.) regarding new features on ShapeWorks (future use of template/sample dataset with fixed particles...)


  • ARCTIC now available as a Slicer3 extension on mac
    • MRML scenes creation with snapshots for improved QC (see pics above)
    • Source code development: other options...
  • Particle correspondence: met with Manasi and Beatriz to include new features
  • Attended QA breakout session: more tests with code coverage to be added soon on both applications!
  • Attended DTI breakout session to identify steps needed to get a consistent package

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)


  • 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