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