Joerg, Later this evening or tomorrow we'll post a beta that has the fixes for this problem for you to try on Ubuntu. When its ready, the centos6_x86_64 build will appear in this directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/ Nick > Dear freesurfer administrators, > > recently upgraded our system to freesurfer 5.2 on lubuntu 13.04. After the > installation I accounted problems when testing freesurfer. tkmedit did not > display the subject bert, instead an error message was shown: > > tkmedit bert orig.mgz > > =================================== > ERROR: A segfault has occurred. This is not your fault, > : but is most likely an unrecoverable error and has > : made the program unstable. > : > : Please send the contents of the file .xdebug_tkmedit > : that should be in this directory to freesurfer@nmr.mgh.harvard.edu > : > : Now exiting... > : > > > > Content of .xdebug_tkmedit is: > > tkmedit started: Thu May 2 08:44:48 2013 > > /usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz > > $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ > Set user home dir to /home/mrt-physician/subjects > Set subject home dir to /home/mrt-physician/subjects/bert > > Segfault > Importing volume with MRIread > xDebug stack (length: 5) > 04: Volm_ImportData( this=0x284adf70, > isSource=/home/mrt-physician/subjects/bert/mri/orig.mgz ) > 04: Importing volume with MRIread > 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) > 03: Reading data into volume > 02: ParseCmdLineArgs( argc=3, > argv=/usr/local/freesurfer/tktools/tkmedit.bin ) > 02: Loading volume orig.mgz > 01: main() > 01: Parsing command line arguments > 00: > 00: > > As I found in the web this problem seems to be due to mri_convert on > fedora 18 (https://bugzilla.redhat.com/show_bug.cgi?id=905638). This bug > is know reproduced for lubuntu 13.04. The output if mri_convert ist called > is the following: > > cd $SUBJECTS_DIR > mri_convert sample-001.mgz test.mgh > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from sample-001.mgz... > Segmentation fault (core dumped) > > Is there a bugfix? > > Sincerely yours > > Joerg > _______________________________________________ > 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.
