Knut, thanks for testing the other two builds and for filing the report. i noticed they had you run valgrind. if you want, i've put a debug build of mri_convert here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ running it in valgrind i think would output source code line numbers of where its going wrong, which would be a big help. Nick > 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
