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

From NAMIC Wiki
Jump to: navigation, search
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
{|
 
{|
 
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
 
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:HPCSeg_V2.jpg|thumb|320px|Subcortical Segmentation of Rhesus subject]]
+
 
 
|}
 
|}
  
Line 9: Line 9:
 
===Key Investigators===
 
===Key Investigators===
  
* Wake Forest: Bob Kraft, Jim Daunais
+
* BWH: Kilian Pohl
 
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
 
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan
 +
* Kitware: Luis Ibanez
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
Line 17: Line 18:
  
 
<h1>Objective</h1>
 
<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.
  
  
Line 24: Line 31:
  
 
<h1>Approach, Plan</h1>
 
<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.
 
 
 
</div>
 
</div>
  
Line 31: Line 37:
  
 
<h1>Progress</h1>
 
<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
 +
 +
{|
 +
|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
 +
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
 +
|}
 +
 +
* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
 +
  {|
 +
|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|220px|Checker Image of source and target before registration ]]
 +
|[[Image:CheckerAfterreg_Screenshot.png|thumb|220px|Checker Image of source and target after registration]]
 +
|}
  
  

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