PET/MR images are compensated with simplified adaptive algorithms for truncated parts of the body. The compensation adapts to a specific location of truncation of the body or organ in the MR image, and to attributes of the truncation in the truncated body part. Anatomical structures in a PET image that do not require any compensation are masked using a MR image with a smaller field of view. The organs that are not masked are then classified as types of anatomical structures, the orientation of the anatomical structures, and type of truncation. Structure specific algorithms are used to compensate for a truncated anatomical structure. The compensation is validated for correctness and the ROI is filled in where there is missing voxel data. Attenuation maps are generated from the compensated ROI.