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"):
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!
> Freesurfer mailing list
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