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 0.1849 > > While 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. > > > 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: *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 >> <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 >> *MailScanner has detected a possible fraud attempt from >> "na01.safelinks.protection.outlook.com" claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
