The deal with using freesurfer 5.3 and older versions of perl is a little complicated because perlbrew installs older versions of perl under the users home directory, but the mni scripts point to /usr/bin/perl. I will point you to this thread where I explain the additional steps you need to do to make it work:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50383.html

Basically, you want to change the first line of a few of the mni scripts to point to your older version of perl instead of the default version on the system. Use the <subject_name>/mri/mri_nu_correct.mni.log file to determine which scripts are failing.

-Zeke

On 12/08/2016 04:46 PM, William George Henry Collishaw wrote:

Apologies, i had the incorrect freesurfer firing later in the script. It is now working with the dev version But it still stands that downgrading to perl 5.18 did not help when using 5.3 ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Thursday, December 8, 2016 2:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_nu_correct error: Ubuntu 16.04

Can you provide the log file when running with the dev version? It really should work when using the dev version.

On 12/08/2016 04:20 PM, William George Henry Collishaw wrote:

...

Hello Freesurfer Developers,

I'm attempting to run recon-all on Ubuntu 16.04, on failure I am getting the following log:

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig .mgz --o orig_nu.mgz

Linux jupiter 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:48:03 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s M87100718 exited with ERRORS at Thu Dec 8 13:48:35 MST 2016

I googled the issue and found recommendations to use the development version of freesurfer OR downgrade Perl from 5.22 to 5.18.

I tried both of these separately and neither worked. I am still getting the same error.

The recon-all.log is attached​

freesurfer version used with perl 5.18

• freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

freesurfer version used with perl 5.22 - ​ freesurfer-Linux-centos6_x86_64-dev-20161205-aab1c9c

Thanks, William Collishaw​

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