Methods, systems and non-transitory computer readable media for imaging are disclosed. Emission projection data corresponding to a target region of a subject is acquired using an emission tomography system. Additionally, one or more magnetic resonance images of the target region are generated using a magnetic resonance imaging system operatively coupled to the emission tomography system. A partially-determined attenuation map is determined by identifying one or more regions in the partially-determined attenuation map with a designated confidence level based on the magnetic resonance images. Further, a complete attenuation map and/or a complete activity map is reconstructed from the emission projection data using the partially-determined attenuation map as a constraint. One or more images corresponding to the target region are then generated based on the partially-determined attenuation map, the complete attenuation map and/or the complete activity map.
