A hybrid MRI-particle-based therapy system can include as components both a particle radiation therapy system configured to apply a charged particle beam to a region of application in a predetermined direction and also a MRI system including a magnetic field generator for generating a magnetic field in an imaging volume which includes the region of application at the same time that the charged particle beam is applied. The MRI system can be configured with two torroidal magnets or a magnet having apertures to provide access to the region of application for the charged particle beam, and to provide a homogeneous magnetic field in the region of application of the charged particle beam. The particle beam can be positioned to pass through a relatively low-strength portion of the main magnetic B0 field of the MRI system. Related methods of image-guided therapy are also provided by embodiments of the present disclosure.