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
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
That is the same error I got when using Fedora 18 and should be due to the newest version of glibc. Em Qui, 2013-05-02 às 11:46 -0400, Nick Schmansky escreveu:
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.
Jorge and Marco,
The beta of v5.3 I mentioned is now available for centos6_x86_64 here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
Please let me know if it works for you on Fedora 18 and Ubuntu 13. As I understand the problem, it is not with glibc directly, but rather glibc chokes in its strcmp implementation on a NULL pointer being passed to it by a freesurfer function call. We fixed that in this beta release (and other things about which we will post in another email).
Thanks,
Nick
That is the same error I got when using Fedora 18 and should be due to the newest version of glibc. Em Qui, 2013-05-02 Ã s 11:46 -0400, Nick Schmansky escreveu:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Joerg Pfannmoeller -
Marcos Martins da Silva -
Nick Schmansky