If freesurfer is adopting some kind of open-source license (hoorrah!), can we do away with the requirement for a license file?
We use the license file requests to keep track of how many people are using FreeSurfer, so probably not.
Are there any components/dependencies of freesurfer that are not open-source?
When it releases, there won't be. The main requirements are things like the MNI tools, GSL, and tcl/tk/tix/blt, but most of those are installed by default on most Linux distros.
Does anyone have detailed instructions for a) compiling freesurfer? b) installation of freesurfer on debian?
We will include instructions with the release. It will be a standard autoconf setup (configure && make && make install). I'm pretty sure it should compile on Debian without a problem.
Is anyone working on creating a debian package for freesurfer? For that matter, has anyone created any rpm packages for freesurfer?
That isn't in the works right now, but maybe somebody can make packages for their favorite distribution(s) and share with the rest of us. :)
Debian already has a package for minc tools, see http://packages.debian.org/stable/science/minc-tools but this does not include all the MNI tools (eg, n3 and mritotal).
We're currently compiling against 1.4, if that helps you plan ahead.