NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction - Revision history

Vidyaraj at 22:02, 26 June 2008

2008-06-26T22:02:33Z

Vidyaraj at 22:01, 26 June 2008

2008-06-26T22:01:06Z

Vidyaraj at 21:55, 26 June 2008

2008-06-26T21:55:28Z

Vidyaraj at 21:54, 26 June 2008

2008-06-26T21:54:37Z

Vidyaraj at 21:51, 26 June 2008

2008-06-26T21:51:27Z

Vidyaraj at 13:56, 2 June 2008

2008-06-02T13:56:17Z

Vidyaraj at 13:25, 2 June 2008

2008-06-02T13:25:12Z

Vidyaraj: 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...

2008-06-02T13:17:32Z

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...

New page

'''Objective:'''

* Develop an atlas of subcortical structures from normal subject images.

'''Progress:'''

* We are currently developing a subcortical atlas following the methods outlined in
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).
[[Image:HPCSeg_V2.jpg|thumb|250pix|Subcortical Segmentation of Rhesus subject]]

'''Key Investigators:'''

* Wake Forest: Bob Kraft, Jim Daunais
* Virginia Tech: Chris Wyatt, Vidya Rajagopalan

'''Links:'''

@@ Line 9: / Line 9: @@
 ===Key Investigators===
 * BWH: Kilian Pohl
 * Virginia Tech: Chris Wyatt, Vidya Rajagopalan

@@ Line 50: / Line 50: @@
 {|
-|[[Image:Vervet_CorScrnShot.jpg|thumb|320px|Segmentation of major tissue classes in for vervet subject ]]
+|[[Image:Vervet_CorScrnShot.jpg|thumb|220px|Segmentation of major tissue classes in for vervet subject ]]
-|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|320px|Subcortical Segmentation of Rhesus 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|320px|Checker Image of source and target before registration ]]
+|[[Image:CheckerB4Reg_Screenshot.jpg |thumb|220px|Checker Image of source and target before registration ]]
-|[[Image:CheckerAfterreg_Screenshot.png|thumb|320px|Checker Image of source and target after registration]]
+|[[Image:CheckerAfterreg_Screenshot.png|thumb|220px|Checker Image of source and target after registration]]
 |}

@@ Line 21: / Line 21: @@
 The objectives of this project are to:
-# Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
+* Optimize the EM Brain Classifier in Slicer on MRI images of vervets.
-# Segment data from N subjects.
+* 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 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.
+* Optimize hippocampus, putamen and caudate  segmentation  so that volume comparison between states can be performed.

@@ Line 39: / Line 39: @@
 <h1>Progress</h1>
 Prior to the project week:
-# Study data on 8 subjects at two time points (alcohol naive and post-induction) organized
+* 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.
+* GM/WM/CSF atlas will be constructed for the study data.
 During Project Week
@@ Line 46: / Line 46: @@
-Optimized segmentation parameters for vervet data
+* Optimized segmentation parameters for vervet data
-Improved accuracy of subcortical segmentation in rhesus data set
+* Improved accuracy of subcortical segmentation in rhesus data set
 {|
@@ Line 54: / Line 54: @@
 |}
-Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
+* Developed an ITK utility for multiresolution demons registration. (Source code available for download from the NAMIC sandbox)
    {|
 |[[Image:CheckerB4Reg_Screenshot.jpg |thumb|320px|Checker Image of source and target before registration ]]

@@ Line 1: / Line 1: @@
 {|
 |[[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 12: / Line 12: @@
 * BWH: Kilian Pohl
 * Virginia Tech: Chris Wyatt, Vidya Rajagopalan
 <div style="margin: 20px;">
@@ Line 40: / Line 41: @@
 # 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.

@@ Line 10: / Line 10: @@
 * Wake Forest: Bob Kraft, Jim Daunais
 * Virginia Tech: Chris Wyatt, Vidya Rajagopalan
@@ Line 17: / Line 18: @@
 <h1>Objective</h1>
@@ Line 24: / Line 31: @@
 <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>
@@ Line 31: / Line 37: @@
 <h1>Progress</h1>

@@ Line 1: / Line 1: @@
-'''Objective:'''
+{|
-'''Progress:'''
+__NOTOC__
-* We are currently developing a subcortical atlas following the methods outlined in
+===Key Investigators===
-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.
-'''Key Investigators:'''
+</div>
-'''Links:'''
+===References===