Thank you.
I confirm, Annotation works fine. However when trying to load label and select .label file.
I get the following message:

reading colortable from annotation file...



colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)

colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)

ERROR: LabelMarkSurface: label point 181451 exceeds nvertices 181405

[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: --------------------- Error Message ------------------------------------

[0]PETSC ERROR: Signal received!

[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.

[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.

[0]PETSC ERROR: See docs/index.html for manual pages.

[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: Unknown Name on a darwin12. named  by Fri Apr  8 16:47:36 2016

[0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt

[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0




Date: Fri, 8 Apr 2016 11:37:29 -0400
From: fischl@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces

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: fischl@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 <pablonajt@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
>
>       _______________________________________________
>       Freesurfer mailing list
>       Freesurfer@nmr.mgh.harvard.edu
>       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> _______________________________________________ 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.
> 
>

_______________________________________________ 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.