Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin.
One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it. On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > just add "--subject fsaverage_sym" > > btw, that command does not perform FDR > > doug > > On 01/23/2014 01:41 PM, krista kelly wrote: > > Hi all, > > > > I have obtained laterality indices using xhemi analyses and would like > > to use FDR instead of the mri_glmfit-sim suggested in the xhemi > > instructions. I know to get the FDR threshold from tksurfer, but I > > want to restrict the clusters to a certain cluster size. Based on a > > previous thread ( > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html > > ) I think this should be done using mri_surfcluster but I am having > > trouble with the actual commands. I've tried this but it doesn't seem > > to work: > > > > mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 > > --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf > > fsaverage_sym --hemi lh > > > > the error = srcsubjid must be supplied > > > > If I'm performing this on a group file (not individual subject), what > > would I even input as the subjid? Or do I have this totally wrong? > > > > Thanks! > > Krista > > > > > > > > > > _______________________________________________ > > 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. > >
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