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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
