Re: [Freesurfer] recon-all -s bert exited with errors
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 <zkauf...@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 > > > 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 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.
Re: [Freesurfer] recon-all -s bert exited with errors
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 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] recon-all -s bert exited with errors
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 recon-all.log Description: Binary data ___ 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.
