Collaboration/WFU/NonHuman Primate Neuroimaging

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Home < Collaboration < WFU < NonHuman Primate Neuroimaging
Before: Nhpbrainexample.png ProgWeek07NHPResult1.png

This project is part of an NIH-NIAAA funded "Collaborations with National Centers for Biomedical Computing" grant, R01-AA016748-01 "Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI" (Jim Daunais PI).

Key Investigators

  • VT/WFU: Chris Wyatt
  • BWH: Kilian Pohl


The objectives of this project are to:

  1. Optimize the EM Brain Classifier in Slicer on MRI images of rhesus macaques
  2. Develop a custom GM/WM/CSF atlas, bootstrapping from one provided by Martin Styner
  3. Integrate a sub-cortical atlas
  4. Segment data from N subjects in the alcohol naive and post-induction state.
  5. Compare GM/WM volume and ratios between the two states
  6. Compare hippocampus, putamen, and caudate volumes between states

Approach, Plan

We will use the current implementation of the EM Brain classifier in slicer. Using a manual segmentation as an estimate of ground truth in a single subject, we will optimize the EM segmenter parameters over the classification error and running time. The study will be run via VPN on a Sungrid at VT.


Prior to the project week:

  • Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
  • Study data has been skull stripped, ECC masks created, and GM/WM/CSF priors registered to each subject. The ECC masks may need some hand editing and, as a result, the atlas-priors to subject registration is poor in several subjects.

During the project week:

  • Nonlinear registration of atlas priors completed using Slicer
  • Full EM segmentation model accommodating severe coil inhomogeneity completed
  • ITK-based utility to spatially blend prior maps written
  • EMSegmenter parameters partially optimized for a single subject
  • Scripts prepared to run the full study


  • K. M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006.
  • E. V. Sullivan, H. J. Sable, W. N Strother, D. P. Friedman, A. Davenport, H. Tillman-Smith, R. A. Kraft, C. L. Wyatt, K. T. Szeliga, N. C. Buchheimer, J. B. Daunais, E. Adalsteinsson, A. Pfefferbaum, K. A Grant, Neuroimaging of Rodent and Primate Models of Alcoholism: Initial Reports from the Integrative Neuroscience Initiative on Alcoholism, Alcoholism: Clinical and Experimental Research Vol. 29 No. 2 pgs 287-294 Feb 2005.