External Email - Use Caution 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. > <dgr...@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 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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
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