On 02/26/2015 01:46 PM, Janosch Linkersdörfer wrote: > Hi all, > > I experimented with the different flags for mri_surfcluster and have 2 issues > that I don't understand, it would be great if somebody could enlighten me: > > 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would > expect, i.e., only clusters with a minimum vertex-wise p-value > thmin are > shown. When I use 'neg' or 'pos', I get clusters with a minimum value below > thmin. Why is that? By default, the threshold will be adjusted when the --sign is pos or neg by subtracting log10(2.0). This assumes several things: (1) the source is a -log10(p) map, and (2) the pvalue was computed using a two-sided t-test. Under these conditions, subtracting log10(2.0) is like dividing the p-value by 2 (ie, changing it from a two-tailed test to a one-tailed test). If the input map does not meet these criteria, then run with --no-adjust.
> > 2) The FDR correction seems to be very lenient. Using --fdr .05, for example, > I get a thmin of 1.158247. That is probably not correct, right? It all depends on the data. If you have a lot of activation, it can be very lenient. > > The command I use looks somewhat like: > > mri_surfcluster --sd /my/subj/dir --in sig.mgh --subject fsa > verage(_DKT) --hemi lh --annot aparcDKT40 --sum summary.txt --clabel > /path/to/label/lh.cortex.label [--fdr .05 | --thmin 3] --thsign [pos | neg | > abs] > > Thanks, > > Janosch > > > _______________________________________________ > 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 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 . 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.
