On Oct 12, 2016 12:09 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:

The sign depends on how you set up the contrast. If you are using an
FSGD file and have two classes A and B and a contrast [+1 -1], then
positive indicates A>B. The F.mgh is the map of F values which are
unsigned. The gamma.mgh file will have the contrast values themselves
including sign. The sig.mgh will be the -log10(p) signed by the sign of
gamma.mgh at that vertex

On 10/12/2016 02:23 PM, neuroimage analyst wrote:
> 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 <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> try this binary
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
> <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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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