Difference between revisions of "Measuring Alcohol Stress Interaction"

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Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|[[thumb|Segmentation of Vervet Subcortical Structures]]
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Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures
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==Key Investigators==
 
==Key Investigators==
 
* VT: Chris Wyatt, Vidya Rajagopalan
 
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov
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* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
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* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ MRIBiasCorrectionFilter] module by Nicolas Rannou available in NAMIC SandBox, initial testing on rhesus data done
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* GWE set up on SPL Cluster for registration parameter exploration
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* ChangerTracker used to detect change between hippocampus of State0 and State1 of first vervet subject.
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{|
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|[[Image:ChangeTracker_3dScreenShot_0.png|thumb|220px|ChangerTracker output for hippocampus changes between state0 and state1]]
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* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.
  
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  {|
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|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.base.png‎ |thumb|220px|Before bias correction ]]
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|[[Image:Hugo_ICC_SagSlice128_BiasC_5.nii.diff.png‎|thumb|220px|After bias correction]]
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|}
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<h3>In Progress</h3>
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* Working with Xioadong to adapt SkullStripper Module for Vervet Images
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* Explore use of ACPC align prior to rigid registration.
 
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==References==
 
==References==
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* [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NA-MIC NCBC Collaboration: Measuring alcohol and stress interaction]
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* [http://wiki.na-mic.org/Wiki/index.php/EMSegment EM Segment project by Sylvain Jaume and Nicolas Rannou]
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* Tustison N., Gee J. "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction" InsightJournal, 2009 January - June, [http://www.insight-journal.org/browse/publication/640]

Latest revision as of 14:29, 26 June 2009

Home < Measuring Alcohol Stress Interaction


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