Dear. Bruce.
Thanks a lot for your help!
I attached the tar.gz file for mri below.
If you need anything more, let me know.
Thanks, Ji Won replay06_mri.tar.gz https://drive.google.com/file/d/0BxRUime4DPjvdGZjb1ZCOUFSNVU/view?usp=drive_web
2016-03-17 11:40 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ji
that does sound strange! Can you tar and gzip the subject and upload it to our website so I can see if I can replicate the problem?
cheers Bruce
On Thu, 17 Mar 2016, Ji Won Bang wrote:
Dear. Freesurfer experts.
Hi.
I'm having a problem with mris_flatten (version 5.3.0)
Could you please help me fix this problem?
My 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
It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch
/home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d
with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory
When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower
select 3 points along a boundary between upper and lower visual fields
(near
calcarine sulcus) and press "Cut line". Then, select 4 points to define
the
cutting plane: 1 on lower side of the line, 2 on upper side of the line,
3
on the opposite surface (use rotation tool), and 4 to specify which
portion
of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d
So I think I made the patch correctly.
! weird thing that I suspect is that when I click save patch as, the
default
location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf
Could you please help me?
Thanks a lot!
Best, Ji Won
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