[Freesurfer] mris_flatten error: bad vertex

2016-03-19 Thread Ji Won Bang 
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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Re: [Freesurfer] mris_flatten error: bad vertex

2016-03-19 Thread Ji Won Bang 
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

​

2016-03-17 11:40 GMT-04:00 Bruce Fischl :

> 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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>
>
> 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.
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mris_flatten error: bad vertex

2016-03-20 Thread Bruce Fischl 
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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Re: [Freesurfer] mris_flatten error: bad vertex

2018-02-20 Thread Foteini Protopapa 
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

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Re: [Freesurfer] mris_flatten error: bad vertex

2018-02-20 Thread Bruce Fischl 
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
>
>
>
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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
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http://www.partners.org/complianceline . If the e-mail was sent to you in error
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