NIck The MRI_convert with debug information ran correctly aside from the leaks detected by valgrind. I manage to import sample-001,mgz into ernie using mri_convert with debuginfo.
There is more updated info athttps://bugzilla.redhat.com/show_bug.cgi?id=905638. Knut On 30. jan. 2013 17:52, Nick Schmansky wrote: > 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
