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 fischl@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 > >
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