Thank you for that clarification,Doug. VM
On Oct 12, 2016 12:09 PM, "Douglas N Greve" <gr...@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 > > <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 > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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