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 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <gr...@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: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis&data=01%7C01%7CBTH22%40pitt.edu%7Ce59dd79b995c400da33c08d4a2b3d3bb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=F%2BYoNdQhEqF0iWAtpPJ8rbx6sRcEcJQgLwTm7wGUEa0%3D&reserved=0> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7Ce59dd79b995c400da33c08d4a2b3d3bb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=TlpipUOHlI9wBEcBdMHORvLFpGzlav4t4ulwWjmXFDY%3D&reserved=0>
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