Hi Pablo
if it has the extension .label then it is a label not an annotation, and
you should load it as such
cheers
Bruce
On Fri, 8 Apr 2016, pablo najt wrote:
Thank you Bruce for the response.Actually the surface works in freeview just
fine. However my second issue about loading annotation continues.
In freeview I clicked on "Annotations" selected inside "label" folder BA1
and everything Freezes.
Terminal shows endless column of the text below.
Could there be that anything went wrong with the annotations? Any way to
check for this and ideally correct without running entire recon-all again?
Thanks a lot
Pablo
MRISreadAnnotationIntoArray: vertex index out of range: 1667852576
i=6C616265, in_array_size=181405
annot file:
/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1814044716
i=2066726F, in_array_size=181405
annot file:
/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1830843253
i=626A6563, in_array_size=181405
annot file: /Vo
____________________________________________________________________________
From: fis...@nmr.mgh.harvard.edu
Date: Fri, 8 Apr 2016 09:56:46 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Can you check and see if they look ok with freeview? It might just be a
display problem
On Apr 8, 2016, at 9:26 AM, pablo najt <pablon...@hotmail.com> wrote:
Dear FS expert and users,
We are coming across errors on the WM and Gray inflated surfaces.
When trying to open the surfaces with tksurfer as follows (tksurfer
subid lh inflated -gray)
We get only a small part of the cortex displaying.
<Screenshot.jpg>
<Screenshot-1.jpg>
Also when we try file-label-import annotation the following error
occurs:
colortable with 13 entries read (originally
/usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)
Found embedded color table in annotation.
There seem to be no hard failures as recon-all log said "finished
without errors". Also WM and pial surfaces look accurate.
Now we are trying to figure what is that could have caused this for
all subjects.
We have an old instructions for freesurfer saying to to run recon-all
as follows.
run recon -all -s subjID /autorecon -all
As I am not familiar with this way of running recon-all I wanted to
ask if this could have caused the problem consistently across 70~
subjects.
Any advise on this would be greatly appreciated.
Cheers.
Pablo
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