Positron emission tomography (PET) has become an invaluable molecular imaging technique for the non-invasive assessment, quantification and appraisal of various biochemical processes in vivo. The emergence of hybrid imaging techniques, such as PET/CT and PET/MRI, in clinical practice engendered a number of new clinical and research opportunities while improved the quantitative accuracy and diagnostic confidence of PET findings. This dissertation focuses on some of the prevalent challenges encountered in PET/MRI image reconstruction mostly MR-guided photon attenuation correction and bone identification from MR images through further development of current state-of-the-art techniques and the investigation and validation of new algorithms. In particular, this dissertation deals with clinical assessment of MR-guided attenuation correction techniques, improving methods of MR-based attenuation map generation and bone segmentation from MR images in whole-body imaging.