Thank you, Doug.

Regards

Virendra

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, October 12, 2016 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Should I use no-adjust in mri_surfcluster

If all you want to do is fdr correction you can use this program:

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr

On 10/10/2016 07:31 PM, Mishra, Virendra wrote:

> Hi, FreeSurfer Users.

> I am comparing cortical thickness of 2 groups controlled for certain

> variables of no interest.

> My contrast matrix is

> 1 -1 0 0 0 0 0 0 0 0 0 0 to check for group 1 thickness > group 2

> thickness

> I get my sig.mgh and I want to run mri_surfcluster command to correct

> for FDR.

> I am confused as to whether I should use –no-adjust in

> mri_surfcluster. According to the help mri_surfcluster

> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster) :

> I have to use –no-adjust if my sig.mgh is not a log(10) map and

> sig.mgh was created using a one-tailed test.

> Since my contrast is group1>group2 ; I am thinking my sig.mgh is a

> log(10) but a one-tailed. Hence I have to use –no-adjust.

> But then again, mri_glmfit

> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) says if #of

> rows in Contrast matrix is 1 (which is true in my case), then the

> F-test reduces to a two-tailed t-test which means I should not use

> –no-adjust.

> I would appreciate any response regarding this.

> Thanks

> Regards

> Virendra

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Douglas N. Greve, Ph.D.

MGH-NMR Center

greve@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

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