Hello FreeSurfer Developers,
I was trying to run recon-all -all, and it failed roughly 30s after it started running, with the error message being: recon-all -s bert exited with errors.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Platform: Red Hat Enterprise Linux Client Release 5.2 uname -a: Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all.log: see attached
Please let me know how I can fix this. Thank you very much!
Best, Qinggang
What version of perl are you using?
$> perl --version
If its perl 5.20 (or maybe 5.22) than the error you are encountering is because because that version of perl is incompatible with the MNI tools shipped with the version of freesurfer you are using.
The easiest way to remedy the situation is to download and install the development version of freesurfer which fixes this issue and will be included in the upcoming 6.0 release (see "Development Version"):
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-Zeke
On 10/17/2016 12:32 PM, Qinggang Yu wrote:
Hello FreeSurfer Developers,
I was trying to run recon-all -all, and it failed roughly 30s after it started running, with the error message being: recon-all -s bert exited with errors.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Platform: Red Hat Enterprise Linux Client Release 5.2 uname -a: Linux schizo.psych.med.umich.edu http://schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all.log: see attached
Please let me know how I can fix this. Thank you very much!
Best, Qinggang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Zeke,
Thanks for your reply! The issue has been resolved - it was the temp folder on the system running out of space. But thank you very much for your suggestions!
Best, Qinggang
On Tue, Oct 18, 2016 at 10:07 AM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
What version of perl are you using?
$> perl --version
If its perl 5.20 (or maybe 5.22) than the error you are encountering is because because that version of perl is incompatible with the MNI tools shipped with the version of freesurfer you are using.
The easiest way to remedy the situation is to download and install the development version of freesurfer which fixes this issue and will be included in the upcoming 6.0 release (see "Development Version"):
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-Zeke
On 10/17/2016 12:32 PM, Qinggang Yu wrote:
Hello FreeSurfer Developers,
I was trying to run recon-all -all, and it failed roughly 30s after it started running, with the error message being: recon-all -s bert exited with errors.
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Platform: Red Hat Enterprise Linux Client Release 5.2 uname -a: Linux schizo.psych.med.umich.edu http://schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all.log: see attached
Please let me know how I can fix this. Thank you very much!
Best, Qinggang
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
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freesurfer@nmr.mgh.harvard.edu
-
Qinggang Yu -
Z K