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
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