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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