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
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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