I think it needs a -f before the surface On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > Many thanks, yes, it did work well. > > But, than I ran "freeview > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > -viewport 3d" > > and got the following message: > > bash-3.2$ freeview > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > -viewport 3d > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable > > Unrecognized sub-option flag 'annot=aparc.annot'. > > > Freeview has opened, but it showed no results at all:-( > > > What should I do? I read that one has to upgrade the newest > freeview-version? Is it possible to get the newest version without > installing freesurfer again? > > Many thanks! > > Dusan > > > ------------------------------------------------------------------------ > Date: Mon, 28 Sep 2015 11:35:50 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 3_group_comparison > > Did you include the back slashes in your command? If so, remove them > and retry. > > On 9/25/15 7:11 PM, Dusan Hirjak wrote: > > Dear Freesurfer experts, > > I am trying to compare 3 groups (aut, sch, ges) according to > thickness, area and LGI at once (omnibus test). > > I did run the following command: > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out > lh.NSS_3_GR.thickness.15.mgh > > > This step did work properly:-) > > > > Now, Im trying to run the following command, but it does not work: > > > mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd > NSS_3_GR.fsgd dods\ --C contrasts.mtx \ --surf fsaverage lh \ > --cortex \ --glmdir NSS_3_GR.glmdir > > > I got this message: "ERROR: Option--y unknown" > > > What am I doing wrong? > > > Thank you for your help! > > > > Best regards > > > Dusan > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ 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. > > > _______________________________________________ > 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
