With the FS 6 beta version the problem doesn't occur. Cheers, Clara ----- Ursprüngliche Mail ----- Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Gesendet: Dienstag, 3. November 2015 18:03:52 Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Try 6.0.0beta. On 11/03/2015 12:02 PM, Clara Kühn wrote: > Our IT guy said it could be a software problem since he didn't have the > problem and the only difference between out computers was the display. > We have these versions at the institute: > > 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta > Is the first one the dev version? > > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu> > An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Gesendet: Dienstag, 3. November 2015 17:57:50 > Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes > > There was a bug in freeview in FS 5.3.0 that may have caused the crash. > Clara, can you try the dev version of freeview? > > Ruopeng > > On 11/03/2015 11:50 AM, Bruce Fischl wrote: > > > 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" <fis...@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 > > _______________________________________________ > 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 > > > _______________________________________________ > 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 > > _______________________________________________ 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
