We developed and validated a Monte-Carlo-based application (RAYDOSE) to generate patient-specific 3D dose maps on the basis of pre-treatment imaging studies. A CT DICOM image is used to model patient geometry, while repeated PET scans are employed to assess radionuclide kinetics and distribution at the voxel level. In this work, we describe the structure of this application and present the tests performed to validate it against reference data and experiments. We used the spheres of a NEMA phantom to calculate S values and total doses. The comparison with reference data from OLINDA/EXM showed an agreement within 2% for a sphere size above 2.8 cm diameter. A custom heterogeneous phantom composed of several layers of Perspex and lung equivalent material was used to compare TLD measurements of gamma radiation from (131)I to Monte Carlo simulations. An agreement within 5% was found. RAYDOSE has been validated against reference data and experimental measurements and can be a useful multi-modality platform for treatment planning and research in MRT.