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


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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