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Hi,

I used the following commands:

 mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out lhHammers_mith_atlas_n30r83_SPM5surf.mgh --out_type mgh --hemi lh --regheader 0021
srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using .../0021/mri/orig.mgz as target reference.
Reading surface .../0021/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 76207
Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
Dim: 125545 1 1


it creates the .mgh file but when I try to open in in Freeview or tksurfer to check the surface file I get the following error message:


my_computer$ freeview
ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 vertices!
Probably trying to use a scalar data file as a surface!


nquads=65537,  nvertices=0
ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

[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 my_computer.local by boris Sun Jan 27 23:12:45 2019
[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
Segmentation fault


Hoe can I actually check the surface file?

Thanks,
Boris 

Am 25.01.2019 um 17:45 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:

Those are the commands. Can you send the command lines you used and a fuller description of exactly how it is not working?

On 1/25/19 10:56 AM, Boris Rauchmann wrote:

        External Email - Use Caution        

Dear FreeSurfer Developers,

 

I´m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all subjects. I tried mri_vol2surf and then mris_seg2annot but without success so far. What commands would you recommend me to run?

 

Thanks,

Boris


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