2010 Summer Project Week Cortical Thickness Analysis

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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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  Cortical thickness on white matter surface

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  Sucal depth on genus-zero cortical surface

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  Particles on inflated genus-zero cortical surface

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 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:

• 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 ShapeWorks development (use of template/sample dataset with fixed particles...)

Progress

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

• 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