On 29. jan. 2013 21:16, Nick Schmansky wrote: > does v5.1 work on this system? no
> does the centos4_x86_64 v5.2 build work? no. I have filed a bug report on https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem with mri_convert and glibc interaction. Knut J > > n. > > On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote: >> Hi Nick >> >> I reran dicom import from /usr/local/freesurfer/subject/sample*. I had >> 24254940 kB free memory but I still got a segmentation error.I used >> sample data from /usr/local/freesurfer/subject. Do you think it is a >> glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64. >> >> >> This error showed up in my dmesg log. >> >> [ 175.413292] mri_convert[1350]: segfault at 0 ip 00000037e092fbda sp >> 00007fff0a9dc2c8 error 4 in libc-2.16.so[37e0800000+1ad000] >> >> >> Knutj >> >> >> >> On 29. jan. 2013 19:47, Nick Schmansky wrote: >>> Knut, >>> >>> I noticed in the log that there was only 284KB of free memory available, >>> which is not enough to run freesurfer, although it would seem like it >>> should be enough to run the mri_convert command. Can you free-up more >>> memory and re-run? Also, I noticed that you're running the Centos6 >>> build, what OS are you running? Fedora 18? Does the v5.2 Centos4 >>> freesurfer build work on that? >>> >>> Nick >>> >>> On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: >>>> When I run recon-all using freesurfer 5.2 latest beta it will segment >>>> crash. >>>> >>>> Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 >>>> x86_64 x86_64 x86_64 GNU/Linux >>>> /home/knutjbj/freesurfer/ernie >>>> >>>> mri_convert /usr/local/freesurfer/subjects/sample-001.mgz >>>> /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz >>>> >>>> mri_convert /usr/local/freesurfer/subjects/sample-001.mgz >>>> /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz >>>> Segmentation fault >>>> Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC >>>> 2013 x86_64 x86_64 x86_64 GNU/Linux >>>> >>>> recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 >>>> >>>> For more details, see the log file >>>> /home/knutjbj/freesurfer/ernie/scripts/recon-all.log >>>> To report a problem, see >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> Knut J >>>> _______________________________________________ >>>> 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
