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