Although these tools often are used alone as described, for common analysis streams it makes sense to incorporate the tools as needed into shell scripts.
A relatively general analysis stream is described here which uses an initialization file to define command options and paths for initialization files and structural brain templates. Goals of these scripts are automation, self-documentation, and generality across species/templates/atlases.
A specific analysis stream for microPET studies is described here that assumes imaging of more than one subject simultaneously.