Hi Clara

that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas?

Bruce

On Tue, 3 Nov 2015, Clara Kühn wrote:

Hi Bruce,

I attached the wm.mgz from one of my participants. It happens with any participant though.
What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentioned error message.

Cheers, Clara

----- Ursprüngliche Mail -----
Von: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 3. November 2015 14:42:25
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Hi Clara

can you send us the wm.mgz and tell us exactly what you did to make it
crash?

thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:

Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes.

I've tried different computers (same FS version) and on some it works and on some the same problem occurs. I just tried it on the 6.0.0beta version and it saved like a charm. I would rather, however, keep editing my data with the same version.
Here is the error message I get in the terminal:

[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 linux-gnu named etsch by ckuehn Fri Oct 30 17:22:55 2015
[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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 (core dumped)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

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