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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