1. A radiation therapy planning and follow-up system, comprising: a magnetic resonance (MR) scanner with a first bore which defines an MR imaging region configured to receive a subject along an MR longitudinal axis; a second imaging scanner with a second bore which defines a second imaging region configured to receive the subject along a second longitudinal axis, the second longitudinal axis being aligned with the MR longitudinal axis; and a radiation therapy type couch configured to move linearly through the MR and second imaging regions and configured to position the subject sequentially in the MR and second imaging regions, the radiation therapy type couch including a tabletop surface and mounting structures configured to accept restraint device which reproducibly constrain a subject in a selected, fixed position with an extremity elevated; wherein the first and second bores have a diameter of at least 70 cm to accommodate a subject constrained on the tabletop surface with the elevated extremity; a plurality of registration marks disposed at least one of on the flat tabletop surface, incorporated in the radiation therapy type couch, on the restraint devices or on the subject; a registration system configured to determine the location of the registration marks in three dimensions with the subject in each of the first bore and the second bore and generate a feedback signal which instructs at least one of an MR scan controller and a second imaging scanner scan controller to adjust a position of the radiation therapy type couch and/or slice or slab positions for aligned image acquisition; a fusion processor configured to combine an image representation generated from data collection in the MR imaging region and an image representation generated from data collection in the second imaging region into a composite image representation; and a planning processor configured to generate a radiation therapy treatment plan according to the composite image; wherein the second scanner includes a PET scanner, the PET scanner with a PET bore which defines a PET imaging region including: a ring of optical detectors dispose adjacent to the PET imaging region optical coupled to a scintillator layer, the ring of optical detectors being configured to generate nuclear imaging data in response to emitted radiation in the PET imaging region; and a heater configured to heat the scintillator; and a controller configured to place the PET scanner in a quiescent mode in which the PET scanner does not emit electrical or RF noise during MR imaging and returns the PET scanner to an active mode after the MR imaging including controlling the heater to heat the scintillator layer to an operating temperature.