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.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32951.html

yes, that is correct

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://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

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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