2009 Winter Project Week:LocalCorticalThicknessPipeline

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Regional cortical thickness analysis on white matter surface
Regional cortical thickness analysis on grey matter surface

Key Investigators

  • UNC: Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz
  • GE: Jim Miller


We are developing an end-to-end application within Slicer3 allowing individual and group analysis of local 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 plan for the project week is to improve the pipeline and focus on the following steps:

  • Mesh inflation with mesh correction
  • Inflated mesh correspondence using particle systems

We will perform the analysis on a small dataset.


The local cortical thickness pipeline has been slightly modified to include WMMap fixing

  • The mesh inflation step has been updated to detect vertices that have a high curvature (extremities)
  • A new module has been developped to correct the WMMap image
  • Pipeline loops until the fixing is no longer necessary

Meetings (with Martin, Dan Marcus, Wendy Plesniak) and concerning future integration of the tool within Slicer3: use of XNAT for group analysis.