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
Hi Knut
does it segfault on other systems? Can you email me the 001.mgz and I'll see if it works here?
thanks Bruce
On Tue, 29 Jan 2013, 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
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
it's probably not enough to run gunzip, which for some reason takes *lots* of ram On Tue, 29 Jan 2013, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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.
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.
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.
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Knut J Bjuland -
Nick Schmansky