2009 Summer Project Week Slicer3 Cortical Thickness Pipeline

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Home < 2009 Summer Project Week Slicer3 Cortical Thickness Pipeline

Key Investigators

  • UNC: Clement Vachet, Cedric Mathieu, Ipek Oguz, Marc Niethammer, Heather Cody Hazlett, Martin Styner


We would like to create end-to-end applications within Slicer3 allowing individual and group analysis of regional (voxel-based) and local (mesh-based) 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:

Our plan for the project week is to:

  • Improve ARCTIC's integration within Slicer3
    • ARCTIC's availability using Slicer3's extension manager interface
    • Cortical thickness overlaid on VTK surface (quality control using Slicer3 MRML scene)
    • Future directions:
      • Batch-processing within Slicer3 to perform group analysis
      • Use of XNAT to directly download atlases needed for processing.
  • Continue on the mesh-based cortical thickness pipeline.
    • Particle correspondence individual testing
    • Automated processing of small pediatric dataset

We are also interested in learning about batch-processing within Slicer3, XNAT integration for future improvment.



  • 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. 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
  • 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 2009 abstract