Ubuntu 16 comes with a version of perl that is compatible 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 09:28 AM, Burkhard Maess wrote: > hello Freesurfer developers, > > during the recon-all (autorecon1) processing, it seems that the > mne_nu_correct procedure does not always manage to finish successfully. I > have searched the net, found a question in the mailing list, which seemed to > be similar, but no answer > (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html). > > Our status file shows, that we had sometimes runs which were completed > without errors. Maybe, we should not have started the recon-all a second > time. It would be very great if you could help with further hints. For > instance, could we remove a file or several files to roll back to the > situation when it worked? > > all the best, > Burkhard > > ..................... > > FREESURFER_VERSION: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 > Platform: ubuntu 16.04 (xfce) >> uname -a > Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 > x86_64 x86_64 GNU/Linux > > Command: > freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 > -nuintensitycor-3T -subjid is09 > > > > > -- > Dr. Burkhard Maess > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig > Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess > 'at' cbs.mpg.de, http://www.cbs.mpg.de > > > > _______________________________________________ > 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.
