2010 Summer Project Week Cortical Thickness Analysis

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Key Investigators

  • UNC: Yundi Shi, Martin Styner
  • Emory: Mar Sanchez

Objective

To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys


Approach, Plan

    • Skull stripping and Tissue segmentation

ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images. Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

    • Affine alignment

RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

    • Atlas building

Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

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
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