you can try recon-all -make all for that subject and and see if it doesn anything. But run mris_euler_number on those surfaces and see if they match. They should all have the same number of faces/edges/vertices (for one hemisphere in the same subject)
On Tue, 22 Mar 2016, Ji Won Bang wrote: > Dear. Bruce. > > Thank you for your advice. > I think I misunderstood what you meant. > > What I did is this. > I showed the contrast result on a surface by using the command: > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast > HorVer > > Then I cut line, and then plane (occipital plane) and save it(3d) as > lh.oc.patch.3d > under $SUBJECTS_DIR/$SUBJECT/surf/ > > I'm not sure if I regenerated the surface files correctly but I believe I > created the > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process. > > > Should I do something else to regenerate the surface? > > Thank you. > > Best, > Ji Won > > > > > > 2016-03-22 11:39 GMT-04:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > what surface did you recut it from? Can you run mris_euler_number on > that > surface (presumably the inflated) and also on the white/orig/pial > surfaces? They should all have the same number of vertices, but I > suspect > some of them won't, meaning that they need to be regenerated. > > cheers > Bruce > > > > > On Tue, 22 Mar 2016, Ji Won Bang wrote: > > > Dear. Freesurfer experts. > > > > Hi. How are you? > > > > I'm trying to flatten the visual cortex using the command mris_flatten > (freesurfer > > version 5.3.0). > > > > The command line is: > > mris_flatten -w 0 -distances 12 7 > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d > > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat > > > > The error I get is: > > using write iterations = 0 > > sampling 7 neighbors out to a distance of 12 mm > > reading patch > /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with > > 27964 vertices (19.0% of total) > > MRISreadPatch: bad vertex # (147220) found in patch file > > No such file or directory > > > > Previously, Bruce advised me to recut it, so I deleted the > lh.oc.patch.3d and recut > > it. However, freesurfer gives me the same error message... > > > > Could you please help me fix it? > > > > Thank you so much. > > > > Best, > > Ji Won > > > > > _______________________________________________ > 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
