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 <gr...@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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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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