SPM and FreeSurfer are similar in the sense that both are morphometry tools.
However, they belong to different kinds.
SPM implements voxel-based morphometry while FreeSurfer represents surface-based morphometry. It is really difficult to do an objective choice here. I don't know a truly impartial comparison of both methods. As a disclaimer, I should say that I prefer surface-based morphometry, and I would suggest as a comparison for you the PDF An Absolute Beginner’s Guide to Surface- and Voxel-based Morphometric Analysis and, as it is written by researchers at the home of FreeSurfer, it is somewhat inclined to FreeSurfer's approach. But its references are good for both SPM and FreeSurfer if you want to know them better.
Putting morphometric technicalities aside, other aspect setting them apart is that SPM is a MATLAB toolbox, so despite being free, it relies on a non-free software. SPM project, under request, are able to provide a standalone version, but this precludes contributed SPM toolboxes. This can be an option when core SPM is enough for your needs. Regarding FreeSurfer, it can be used on a mostly free platform (not free as in Free Software Foundation's sense but more like what you would find in Ubuntu's based software). FreeSurfer runs natively on POSIX-like operating systems (Linux and MacOS) and the project has virtual machine images for VirtualBox, so Windows users can run a virtualized XUbuntu with FreeSurfer installed.
Finally, in terms of integration with R, FreeSurfer project lacks an official integration as it tries to be self contained and includes some statistical analysis capabilities on its own. I have used R to analyze data from FreeSurfer and it wasn't particularly difficult as it is stored in textual form. I heard about an R package, freesurfR — I don't know if it is still maintained — that could do some things in a two-way fashion.
SPM, being aimed at MATLAB, makes an integration with R a somewhat challenging manual task. I heard about an attempt to implement it in R, by means of a package called spmR. When I have used SPM, I had access to a licensed MATLAB and R integration was not that important so I have not insisted. Perhaps it can be done on a more natural way.
In the context of my Master's, FreeSurfer was our choice.