Hi

I am using recon-all in some longitudinal data on a ubuntu 16.04, and using the development version of freesurfer as I was told here, because the other current version doesnt work on ubuntu 16.04.

The problem is that the first scans were probablly processed using virtualbox in a windows and an older version of freesurfer.

i think I already know the answer, that I can't do this if I dont want to bias my results. Can I?

Yup. You know the answer ;) However, I did discover a way to make freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install an older version of perl :

1) install perlbrew:

$> sudo apt-get install perlbrew

2) use perlbrew to install perl version 5.20.3:

$> perlbrew install perl-5.20.3

3) You must change the '/bin/perl' file to a link which points to the version of perl installed by perlbrew. (This technique is not the standard practice but it is the only way to get the mni tools to use the older version of perl):

$> cd /bin $> sudo mv perl perl.orig (can always set back later) $> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl

But I'm using a better computer now and I use the one with windows for other analyses, so I wanted to know if I could install Virtual box on my ubuntu 16.04 computer, and install the same version of linux used to process the first measure. Should I also need to use the same version of freesurfer?

You could do that, but The Virtual Box version is not really good for processing a large number of subjects because of the limited amount of disk space on the virtual image. Its really meant more as a teaching tool for users with Windows machines.

f the computer's specs are dfferent, does it matter? And if I assign different cpu and ram on my virtual machine?

Different specs are fine. Its the OS, OS version, and version of freesurfer that should stay the same.

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