does v5.1 work on this system? does the centos4_x86_64 v5.2 build work?
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
