Measuring Alcohol Stress Interaction

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  Projects List

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  Segmentation of Vervet Subcortical Structures

Key Investigators

• VT: Chris Wyatt, Vidya Rajagopalan
• BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

Objective

• To improve cortical segmentation of Vervet segmentation Results
• Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

Approach, Plan

• Improve rigid registration results by optimizing parameters
• Add bias correction to workflow to improve segmentation results
• Study hippocampal changes between subjects at two time points using Change Tracker

Progress

• ChangeTracker augmented with the capability to accept externally-defined segmentation (ChangeTrackerVT in NAMIC Sandbox)
• MRIBiasCorrectionFilter module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
• GWE set up on SPL Cluster for registration parameter exploration
• ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.

ChangerTracker output for hippocampus changes between state0 and state1

• MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.

Before bias correction

After bias correction

In Progress

• Working with Xioadong to adapt SkullStripper Module for Vervet Images
• Explore use of ACPC align prior to rigid registration.

References

• NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction
• EM Segment project by Sylvain Jaume and Nicolas Rannou
• Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [1]