Okay but if we run a simple regression analysis on the mean values between groups for the clusters which mri_glmfit-sim found significant between groups, why isn't that significant? Are we leaving a covariate out?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Friday, May 26, 2017 12:50:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Contrast matrix format {Disarmed}
It does not matter whether you used the maxvox or the mean of the cluster. The two p-values are measuring fundamentally different phenomena. The cluster pvalue is measuring the likelihood of seeing a cluster of that size by chance. The p-value you have computed is the likelihood of seeing a mean value in the cluster greater than 0.
On 05/26/2017 12:43 PM, Hilton, Benjamin Taylor wrote:
I was trying to follow along with the suggestion you provided someone else here: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-arc...
I'm not sure how relevant that solution is to my problem though, and I'm pulling values from the "cache.th40.neg.y.ocn.dat" file which is output by the mri_glmfit-sim method. I believe this has the mean cluster value for each subject and each cluster. I am comparing the p-values to the cluster wise p-values.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* Thursday, May 25, 2017 6:06:30 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Contrast matrix format {Disarmed} Not sure what you did. Sound like you found the max vox from the cluster, then extracted the values from each subject and ran those values through the glm to compare p-values against those in the summary file. Right? Now, which values from the summary file are you comparing against? The cluster-wise p-value is the p-value of the cluster, not of a voxel in the cluster. The cluster p-values is the chance that you see a cluster of that size by chance.
On 05/25/2017 03:06 PM, Hilton, Benjamin Taylor wrote:
Running that code it turns up these values:
pvalues =
1.0e-04 *
0.2084 0.1849While the p-values are 0.1340 and 0.02200 respectively in the summary file, why the difference?
*From:* Hilton, Benjamin Taylor *Sent:* Thursday, May 25, 2017 2:43:35 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Contrast matrix format
After some digging I found this thread where someone was having a similar issue, so I can give this matlab code you posted a try.
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-arc...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Wednesday, May 24, 2017 10:47:24 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Contrast matrix format
yes, that is correct
On 5/24/17 10:38 AM, Taylor Hilton wrote:
Hi all,
I’m trying to perform a group analysis according to the tutorial on this page: *MailScanner has detected a possible fraud attempt from "na01.safelinks.protection.outlook.com" claiming to be*
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr....
For my own analysis, I have 4 total groups, and I’m trying to do a contrast between two of those groups.
My matrix file is formatted ‘0 1 -1 0’, since I’m trying to contrast the 2nd and 3rd groups.
My fsgd file is formatted as the following: GroupDescriptorFile 1 Title PYSCan Class 1 Class 2 Class 3 Class 4 Input s70032 2 Input s70038 1 …
Wanted to verify that this is correct since there doesn’t appear to be a group difference when comparing the clusters against the rest of the data.
Any help is very appreciated!
Sincerely, B. Taylor Hilton Lab Data Coordinator University of Pittsburgh
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