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: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32951.html > > > 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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@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 0.1849 > > > > 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. > > > > > > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32951.html&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=XWWDmJEGLqPk68a1730xVmNBLROYJNCnQGeSxtlNm1s%3D&reserved=0 > > > > ------------------------------------------------------------------------ > > *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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=0TekDrngIQuxBzm7%2BfH%2Bl0duFB7dzd1zHsqb9ESgNpM%3D&reserved=0 > > > >> > <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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=hAPzusEDuX5MjF2ynCXP5xIgvR780W4DXIeCEB%2FI6EM%3D&reserved=0 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=hAPzusEDuX5MjF2ynCXP5xIgvR780W4DXIeCEB%2FI6EM%3D&reserved=0 > > -- > 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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=RWH3boZW1c8eTSGdxAYwFkXVfO3JIYYc02M2Wi3UM3c%3D&reserved=0 > https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=oA7%2FyUp16f%2BYbk%2BWECPlWDsJlWX9FKGVOI2s%2FDFIDUY%3D&reserved=0 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=hAPzusEDuX5MjF2ynCXP5xIgvR780W4DXIeCEB%2FI6EM%3D&reserved=0 > > > 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 > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=01%7C01%7CBTH22%40pitt.edu%7C1ff1026c69bb4920a63108d4a3ba5aea%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=2PCOtJdpRul4EWXYkkpYhRbSNKJiMLWXi%2BDfSMu9Jto%3D&reserved=0 > > . 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. > > > > _______________________________________________ > 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.
