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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@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-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32951.html&data=01%7C01%7CBTH22%40pitt.edu%7C162aa8b59e2d486a45eb08d4a4574e88%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=UCKGxK2ewtC%2FzM%2BAbSKS2Ths5fJkGft1SxDX1ezEwQg%3D&reserved=0
>
>
> 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
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> >>
> <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
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> >
> >
> >
> > _______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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