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 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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
>     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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