Particle radiation therapy and planning utilizing magnetic resonance imaging (MRI) data. Radiation therapy prescription information and patient MRI data can be received and a radiation therapy treatment plan can be determined for use with a particle beam. The treatment plan can utilize the radiation therapy prescription information and the patient MRI data to account for interaction properties of soft tissues in the patient through which the particle beam passes. Patient MRI data may be received from a magnetic resonance imaging system integrated with the particle radiation therapy system. MRI data acquired during treatment may also be utilized to modify or optimize the particle radiation therapy treatment.