One embodiment of the present invention provides an integrated PET-MRI scanner. This integrated scanner includes a main magnet that generates a magnetic field, wherein images of the subject is generated in a central region of the magnetic field. It also includes a PET scanner which is enclosed by the main magnet. The PET scanner further comprises: (1) at least one ring of scintillators, which is situated in the central region of the magnetic field and, (2) one or more photodetectors, which are coupled to the ring of scintillators, so that the one or more photodetectors are outside the central region of the magnetic field. The integrated scanner also includes radio-frequency (RF) coils which are enclosed by the PET scanner. By keeping the photodetectors and associated circuitry outside the central region of the magnetic field, the integrated scanner reduces the electromagnetic interference (EMI) between the PET scanner and the MRI scanner.