Imaging system and method are presented. Emission scan (ES) and anatomical scan (AS) data corresponding to a target volume in a subject are received. One or more at least partial AS images are reconstructed using AS data. An image-space certainty (IC) map representing a confidence level (CL) for attenuation coefficients of selected voxels in AS images and a preliminary attenuation (PA) map based on AS images are generated. One or more of selected attenuation factors (AF) in projection-space are initialized based on PA map. A projection-space certainty (PC) map representing CL for the selected AF is generated based on IC map. An emission image of the target volume is initialized. The selected AF and emission image are iteratively updated based on the ES data, PC map, initial AF, and/or initial emission image. A desired emission image and/or AF values are determined based on the iteratively updated AF and/or emission image.