Difference between revisions of "NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction"

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(New page: '''Objective:''' * Develop an atlas of subcortical structures from normal subject images. '''Progress:''' * We are currently developing a subcortical atlas following the methods outline...)
 
 
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'''Objective:'''
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{|
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|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
  
* Develop an atlas of subcortical structures from normal subject images.
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'''Progress:'''
 
  
* We are currently developing a subcortical atlas following the methods outlined in
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__NOTOC__
M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE  Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8.
 
  
* Below is a snap shot of subcortical segmention of one of the subjects. The hippocampus, caudate and putamen are clearly visible (marked in blue, yellow and indigo) amidst the gray matter(marked in red) and WM (marked in green).
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===Key Investigators===
[[Image:HPCSeg_V2.jpg|thumb|250pix|Subcortical Segmentation of Rhesus subject]]
 
  
'''Key Investigators:'''
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* BWH: Kilian Pohl
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* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
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* Kitware: Luis Ibanez
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<div style="margin: 20px;">
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<div style="width: 27%; float: left; padding-right: 3%;">
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<h1>Objective</h1>
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The objectives of this project are to:
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* Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
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* Segment data from N subjects.
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* Optimize GM/WM/CSF segmentation so that  calculation of GM/WM volume and ratios between the two states can be automated.
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* Optimize hippocampus, putamen and caudate  segmentation  so that volume comparison between states can be performed.
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</div>
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<div style="width: 27%; float: left; padding-right: 3%;">
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<h1>Approach, Plan</h1>
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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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</div>
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<div style="width: 40%; float: left;">
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<h1>Progress</h1>
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Prior to the project week:
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* Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
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* GM/WM/CSF atlas will be constructed for the study data.
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During Project Week
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* Optimized segmentation parameters for vervet data
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* Improved accuracy of subcortical segmentation in rhesus data set
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{|
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|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
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|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
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|}
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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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  {|
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|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|220px|Checker Image of source and target before registration ]]
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|[[Image:CheckerAfterreg_Screenshot.png|thumb|220px|Checker Image of source and target after registration]]
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|}
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</div>
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<br style="clear: both;" />
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</div>
  
* Wake Forest: Bob Kraft, Jim Daunais
 
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
 
  
'''Links:'''
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===References===
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*

Latest revision as of 22:02, 26 June 2008

Home < NA-MIC < Projects < External Collaboration < Measuring Alcohol and Stress Interaction



Key Investigators

  • BWH: Kilian Pohl
  • Virginia Tech: Chris Wyatt, Vidya Rajagopalan
  • Kitware: Luis Ibanez

Objective

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.


Approach, Plan

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.

Progress

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
Segmentation of major tissue classes in for vervet subject
Subcortical Segmentation of Rhesus subject
  • Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
Checker Image of source and target before registration
Checker Image of source and target after registration




References