View source for NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction

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===Key Investigators===

* Wake Forest: Bob Kraft, Jim Daunais
* BWH: Kilian Pohl
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
* Kitware: Luis Ibanez

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<h1>Objective</h1>

The objectives of this project are to:
* Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
* Segment data from N subjects.
* Optimize GM/WM/CSF segmentation so that  calculation of GM/WM volume and ratios between the two states can be automated.
* Optimize hippocampus, putamen and caudate  segmentation  so that volume comparison between states can be performed.


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<h1>Approach, Plan</h1>
We will use the current implementation of the EM Segmenter 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.
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<h1>Progress</h1>
Prior to the project week:
* Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
* GM/WM/CSF atlas will be constructed for the study data. 

During Project Week

 

* Optimized segmentation parameters for vervet data
* Improved accuracy of subcortical segmentation in rhesus data set

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|[[Image:Vervet_CorScrnShot.jpg|thumb|320px|Segmentation of major tissue classes in for vervet subject ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]]
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* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
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|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|320px|Checker Image of source and target before registration ]]
|[[Image:CheckerAfterreg_Screenshot.png|thumb|320px|Checker Image of source and target after registration]]
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===References===
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