Hi Rebecca,

Are you talking about the pulse sequence or analysis software, like FSL or SPM?  Siemens scanners come with an EPI sequence which should be fine for fMRI.  To do the analysis, people usually move the data to a remote computer where they have the analysis software installed.  Installing additional software on the host computer of the scanner would most likely void your warranty or service contract.  I am not sure about all versions of Siemens' software, but at least the more current versions do have some tools for fMRI analysis built in, but in research people normally use dedicated software like FSL, SPM or AFNI.

Good Luck,
Allen