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
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
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
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.
Dear FreeSurfer Experts,
Can somebody tell me if there is a solution to this mris_flatten error?
I get...
MRISreadPatch: bad vertex # (144585) found in patch file
and is not about how I save my patch or where. I have done it another 82 times
and everything worked perfectly. Any insights/ suggestions are welcome.
Regards,
Foteini Protopapa
Hi Foteini
we need a lot more information. How did you create the patch? What was your command line and full screen output? What version of FS are you using?
cheers Bruce On Tue, 20 Feb 2018, Foteini Protopapa wrote:
Dear FreeSurfer Experts,
Can somebody tell me if there is a solution to this mris_flatten error?
I get...
MRISreadPatch: bad vertex # (144585) found in patch file
and is not about how I save my patch or where. I have done it another 82 times
and everything worked perfectly. Any insights/ suggestions are welcome.
Regards,
Foteini Protopapa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Foteini Protopapa -
Ji Won Bang