View source for Measuring Alcohol Stress Interaction

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:MonkeyProject09Slicer.png|Segmentation of Vervet Subcortical Structures
Image:ChangeTracker_3dScreenShot_0.png|ChangerTracker output for hippocampus changes between state0 and state1
</gallery>



==Key Investigators==
* VT: Chris Wyatt, Vidya Rajagopalan
* BWH: Andrey Fedorov, Ron Kikinis, Nicolas Rannou, Sylvain Jaume

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* To improve cortical segmentation of Vervet segmentation Results
* Use Change tracker module in Slicer to study hippocampal changes between subjects at two time points

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* 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

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
* ChangeTracker augmented with the capability to accept externally-defined segmentation ([http://svn.na-mic.org/NAMICSandBox/trunk/ChangeTrackerExtra/ChangeTrackerVT/ ChangeTrackerVT] in NAMIC Sandbox)
* [http://svn.na-mic.org/NAMICSandBox/trunk/MRIBiasCorrectionFilter/ 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.
* MRIBiasCorrection Module parameter exploration being set up in GWE of SPL cluster.
<h3>In Progress</h3>
* Working with Xioadong to adapt SkullStripper Module for Vervet Images
</div>
</div>
<div style="width: 97%; float: left;">

==References==
* [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]
* [http://wiki.na-mic.org/Wiki/index.php/EMSegment 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, [http://www.insight-journal.org/browse/publication/640]