2009 Summer Project Week FunctionalClusteringAnalysis - Revision history

Dougt: /* Key Investigators */

2009-06-26T13:49:48Z

Key Investigators

Dougt: /* Key Investigators */

2009-06-22T17:57:58Z

Key Investigators

Dougt at 17:26, 22 June 2009

2009-06-22T17:26:20Z

Dougt: /* Key Investigators */

2009-06-22T17:11:24Z

Key Investigators

Tkapur at 02:03, 22 June 2009

2009-06-22T02:03:23Z

Dougt at 19:15, 16 June 2009

2009-06-16T19:15:11Z

Dougt: Created page with 'NOTOC Image:PW2009-v3.png|Project Week Main Page ==Key Investigators== * BWH: Doug Terry, Marek Kubicki, Andrew Rausch, Lau...'

2009-06-16T18:12:35Z

Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Doug Terry, Marek Kubicki, Andrew Rausch, Lau...'

New page

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Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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==Key Investigators==
* BWH: Doug Terry, Marek Kubicki, Andrew Rausch, Lauren O'Donnell, David Tate

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<h3>Objective</h3>
We are using the clusters that are automatically outputted from whole-brain tractography and whole-brain congealing/clustering to draw correlations based on anatomical connectivity to see if there are group differences between chronic schizophrenics and controls.

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<h3>Approach, Plan</h3>

After whole brain tractography is completed for each case, the tracts for all the cases will be put through group coregistration/congealing. Then clustering takes place on the mean congealed brain. Specified number of clusters here is 200 for the whole brain. The clusters from the mean image are then transferred back to individual subject space. The mean FA/Mode/Trace will be taken from each cluster on each subject.

These diffusion values will then be correlated with clinical/neuropsych assessments. This is a way to look at possible deficits in schizophrenics without grouping the entire anatomical cluster together.

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<h3>Progress</h3>
Each case has undergone whole-brain tractography. Group coregistration, congealing, and clustering has also taken place, but there are issues with the validity of the group coregistration in the pipeline. Once this is worked out, the results from the clustering will be more reliable and the measures of diffusion (FA/Mode/Trace/Axial Diffusion/Radial Diffusion) will be extracted.

The most relevant neuropsychological and clinical measures are being selected by David Tate. Correlations between these values and diffusion measures will be run on automatically outputted clusters to see if there are any differences between the 2 subject groups.

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==References==
* [http://lmi.bwh.harvard.edu/papers/papers/odonnellThesis06.html O'Donnell L. Cerebral White Matter Analysis Using Diffusion Imaging. Ph.D. thesis, Massachusetts Institute of Technology, 2006.]
* [http://pnl.bwh.harvard.edu/pub/papers_html/WhitfordMysell2009.html Whitford T, Kubicki M, King R, Khan U, Markant D, Alvarado J, McCarley R, Shenton ME. Abnormalities in tensor morphology in patients with schizophrenia: A dti study of the corpus callosum, 2009.]

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← Older revision		Revision as of 13:49, 26 June 2009
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	For analysis, we are first looking at the data in 2 ways: 1) Within the Normal Controls, we will be measuring FA/Mode/Trace/Axial Diffusion/Radial Diffusion for all the 200 bilateral tracts and correlating them with neuropsychological tests since trends would be expect in a healthy population. 2) Divide each of the 200 clusters down the midsagittal plane to separate the bilateral clusters into left and right sides. Then correlate with neuropsych.		For analysis, we are first looking at the data in 2 ways: 1) Within the Normal Controls, we will be measuring FA/Mode/Trace/Axial Diffusion/Radial Diffusion for all the 200 bilateral tracts and correlating them with neuropsychological tests since trends would be expect in a healthy population. 2) Divide each of the 200 clusters down the midsagittal plane to separate the bilateral clusters into left and right sides. Then correlate with neuropsych.
		+
		+	End of Project Week Update
		+	Diffusion vales are being extracted from the automatically clustered tract files so that Analysis 1 can be completed in the near future. We're also in the process of writing a script to divide the tract files to separate the tracts in the left hemisphere and the right hemisphere so unilateral analyses can be run.

@@ Line 7: / Line 7: @@
 ==Key Investigators==
-* BWH: Doug Terry, Marek Kubicki, Andrew Rausch, Lauren O'Donnell, David Tate, CF Westin
+* BWH: Doug Terry (dougt@bwh.harvard.edu), Marek Kubicki, Andrew Rausch, Lauren O'Donnell, David Tate, CF Westin
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@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
+Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
 Image:Dougt_NAMIC1.jpg|Whole brain clustering in sagittal view.
 Image:Dougt_NAMIC2.jpg|Whole brain clustering in axial view.

@@ Line 26: / Line 26: @@
 <h3>Approach, Plan</h3>
-After whole brain tractography is completed for each case, the tracts for all the cases will be put through group coregistration/congealing. Then clustering takes place on the mean congealed brain. Specified number of clusters here is 200 for the whole brain. The clusters from the mean image are then transferred back to individual subject space. The mean FA/Mode/Trace will be taken from each cluster on each subject.
+After whole brain tractography is completed for each case, the tracts for all the cases will be put through group coregistration/congealing. Then clustering takes place on the mean congealed brain. Specified number of clusters here is 200 for the whole brain, bilaterally. The clusters from the mean image are then transferred back to individual subject space. The mean FA/Mode/Trace will be taken from each cluster on each subject.
 These diffusion values will then be correlated with clinical/neuropsych assessments. This is a way to look at possible deficits in schizophrenics without grouping the entire anatomical cluster together.
@@ Line 35: / Line 35: @@
 <h3>Progress</h3>
-Each case has undergone whole-brain tractography. Group coregistration, congealing, and clustering has also taken place, but there are issues with the validity of the group coregistration in the pipeline. Once this is worked out, the results from the clustering will be more reliable and the measures of diffusion (FA/Mode/Trace/Axial Diffusion/Radial Diffusion) will be extracted.
+Each case has undergone whole-brain tractography. Group coregistration, congealing, and clustering has taken place and the results have been confirmed as anatomically accurate by Lauren O'Donnell. The most relevant neuropsychological and clinical measures are being selected by David Tate. Correlations between these values and diffusion measures will be run on automatically outputted clusters to see if there are any differences between the 2 subject groups.
-The most relevant neuropsychological and clinical measures are being selected by David Tate. Correlations between these values and diffusion measures will be run on automatically outputted clusters to see if there are any differences between the 2 subject groups.
+For analysis, we are first looking at the data in 2 ways: 1) Within the Normal Controls, we will be measuring FA/Mode/Trace/Axial Diffusion/Radial Diffusion for all the 200 bilateral tracts and correlating them with neuropsychological tests since trends would be expect in a healthy population. 2) Divide each of the 200 clusters down the midsagittal plane to separate the bilateral clusters into left and right sides. Then correlate with neuropsych.

2009 Summer Project Week FunctionalClusteringAnalysis - Revision history

Dougt: /* Key Investigators */

Dougt: /* Key Investigators */

Dougt at 17:26, 22 June 2009

Dougt: /* Key Investigators */

Tkapur at 02:03, 22 June 2009

Dougt at 19:15, 16 June 2009

Dougt: Created page with '__NOTOC__ Image:PW2009-v3.png|Project Week Main Page ==Key Investigators== * BWH: Doug Terry, Marek Kubicki, Andrew Rausch, Lau...'

Dougt: Created page with 'NOTOC Image:PW2009-v3.png|Project Week Main Page ==Key Investigators== * BWH: Doug Terry, Marek Kubicki, Andrew Rausch, Lau...'