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
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.