The University of California at San Diego and the Salk Institute established the Center for Functional Magnetic Resonance Imaging in 2002. The center's main goal is to facilitate advanced imaging studies of the physiology and anatomy - from mice to humans. The center houses three imaging systems: two 3T short bore scanners (GE Excite HDx and GE MR750) for human studies (the first one was delivered in 2004 and the second in 2010), and a 7T system (21 cm bore, Bruker Avance II console) for rodent imaging. All systems operate on identical GE software platforms and consoles, and are equipped for state-of-the-art high resolution structural imaging, dynamic imaging (echo planar imaging (EPI) and spiral acquisitions), and proton and phosphorous magnetic resonance spectroscopy (MRS).

The center occupies a new building on the main UCSD campus adjacent to the Basic Science Building where the existing animal handling facility is housed. The facility is approximately 7,000 sq. ft and contains a machine shop, an electronics shop, a conference room, and office space for nine faculty and supporting staff.