How to import images used to analysis in SPM to FreeSurfer
I found help at the FreeSurfer mailing list regarding this question. The answer is that for the structural analysis, there is no need to run the recon-all command in a specific directory structure. 

It is just a matter of running 

recon-all -s SUBJECTNAME -all -i IMAGE.IMG


Note that I am feeding an img file, which is what I am using now, however the creators of the software suggest the use of the DICON filetype.