What p-values are you comparing to? You should run the analysis with 
mri_glmfit.m Are you sure that the design matrix is exactly the same in 
R? The design matrix in Xg.dat



On 05/31/2017 02:10 PM, Hilton, Benjamin Taylor wrote:
>
> Sorry I don't think I've been very clear, got off on a tangent about 
> the program before that sort of sidestepped the original question.
>
>
> We're running a linear regression in R with the individual values from 
> the cache.th40.neg.y.ocn.dat file, with values of one cluster as the 
> dependent variable and our study groups as the independent variable.
>
>
> The R format being lm(cluster ~ groups).
>
>
> This analysis is showing p values well above .05 (.233 and 0.887, for 
> clusters 1 and 2 respectively, of the left hemisphere), even though 
> the clusters are supposed to be significantly different between our 
> groups according to the output of mri_glmfit-sim .  I'd like to know 
> if there's some covariate left out of the analysis, or am I looking at 
> the wrong individual values perhaps?  We are hoping to get the value 
> of the cortical thickness for each individual subject in a 
> specific cluster.
>
> ------------------------------------------------------------------------
> *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 5:38:35 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Contrast matrix format {Disarmed}
> Aren't your p-values sig? They are both in the range of .0001
>
>
> On 05/26/2017 02:23 PM, Hilton, Benjamin Taylor wrote:
> >
> > 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
>  
>
> >
> > >
> > > >>
> > >
> > 
> <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*
> > > >>
> > >
> > 
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> > > >
> > > >
> > > > _______________________________________________
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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
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop:
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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
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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