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
>
>

_______________________________________________
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.