> almost all of the analysis software is closed source This is almost certainly not true. BrainSurfer is closed-source, but almost everything else I can think

> almost all of the analysis software is closed source This is almost certainly not true. BrainSurfer is closed-source, but almost everything else I can think of is open-source. * SPM is available under the GPL: http://www.fil.ion.ucl.ac.uk/spm/software/ http://www.fil.ion.ucl.ac.uk/spm/software/ * FSL (including the source) is available under their own noncommercial "As-Is" license. FSLView seems to have its own separate GPL license: http://fsl.fmrib.ox.ac.uk/fsldownloads/ http://fsl.fmrib.ox.ac.uk/fsldownloads/ * AFNI used to require (free) registration, but is now GPL: https://afni.nimh.nih.gov/afni/about/legal https://afni.nimh.nih.gov/afni/about/legal * The BIC-MNI tools + source appear to be freely available for free under an "as-is" + attribution license. I only checked a few; please let me know if any are not and I will nag people accordingly: https://github.com/BIC-MNI https://github.com/BIC-MNI * Caret is GPL: http://brainvis.wustl.edu/wiki/index.php/Caret:About http://brainvis.wustl.edu/wiki/index.php/Caret:About * FreeSurfer has its own license which is very open: http://www.freesurfer.net/fswiki/FreeSurferSoftwareLicense http://www.freesurfer.net/fswiki/FreeSurferSoftwareLicense I suspect you're thinking of this, which reported differences between FreeSurfer versions: http://journals.plos.org/plosone/article/comment?id=info%3Adoi%2F10.1371%2Fannotation%2F2054bfcc-614f-4fe0-b1e4-72b6e89ba8e5 http://journals.plos.org/plosone/article/comment?id=info%3Ad... That turned out to be a combination of 1) algorithmic changes 2) Different random seeds (some of these functions use Monte Carlo-like methods), and 3) 32 vs 64 bit platforms.