The invention comprises a method and apparatus for imaging a tumor with X-rays while, simultaneously or alternatingly, treating or imaging the tumor with positively charged particles. An X-ray imaging system, such as one or two sets of a cone beam X-ray source coupled to an X-ray detector, is rotatable about a first axis and a patient. The X-ray imaging system is positioned off axis a path of charged particles delivered through an exit port of a nozzle system from a synchrotron and does not block a path of the positively charged particles from the exit nozzle to the patient or an imaging path from the patient to a scintillation detector. Fiducial indicators are used to confirm an unobstructed path of the positively charged particles in a treatment room comprising many movable elements, such as the X-ray imaging system and a patient positioning system/couch.