Hello Peter,
I understand your dilemma, its unfortunate the updated version of perl causes the MNI tools to fail. If you MUST use freesurfer 5.3 on an Ubuntu 16 machine there is only one way that I can think of to make it work:
You need to install perlbrew and use that to install perl version 5.20.3:
$> sudo apt-get install perlbrew $> perlbrew install perl-5.20.3
You then must change the first line of any mni script that fails (their should only be a few) to point to the perl v5.20 instead of the default. So for example, the first line of $FREESURFER_HOME/mni/bin/nu_correct should be changed from:
#!/usr/bin/perl -w to: #!~/perl5/perlbrew/perls/perl-5.20.3/bin/perl -w
You may need to do this with a couple of the MNI scripts. I know this is not an ideal solution but it is the only way I know of to get freesurfer5.3 working on Ubuntu 16.
-Zeke
Hi,
there is an old thread about an recon-all error on Ubuntu 16.04, that is caused by an incompatibility between the MNI tools and the perl version 5.22 distributed with Ubuntu 16.04.
This has been fixed in the development version. Has someone a more detailed description how this was fixed so that I could try to back-port this fix to freesurfer 5.3?
Downgrading perl in Ubuntu 16.04 is not possible, there are to many packages depending on it and there is no other version of perl in the repositories.
We have already about 100 subjects analyzed with version 5.3 and I hesitate to re-analyze all of them with the development version.
Since we had to update Ubuntu to 16.04 for other reasons, we use freesurfer 5.3 now inside a virtual machine with Ubuntu 14.04 installed, which is not very efficient.
Peter
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