Thanks, Doug for the binary.

 A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are only positive and p-values obtained from them has sign of +/-. My understanding is + indicates where mean_A>mean_B and vice versa. 

If for example, I am interested in mean_A>mean_B then should I pass --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected cluster defining threshold of p<0.005)  in the contrast that was designed for that test?

Regards

MV

On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
try this binary

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



On 10/07/2016 04:11 PM, neuroimage analyst wrote:
>
> Hi,
>
> I was wondering if there is a way to perform fdr correction using
> command line in freesurfer without using matlab as mri_glmfit-sim only
> does bonferroni ?
>
> Thanks
> Regards
> MV
>
>
>
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