Emission tomography (ET, including PET and SPECT) imaging measures physiological function that is not often accessible from other imaging modalities. Despite its well-demonstrated clinical value, the state-of-the-art ET imaging continues to be affected by two major challenges, inherently noisy data and limited spatial resolution. The spatial resolution is further degraded by involuntary organ motion which cannot be avoided during data acquisition. These challenges are more prominent in dynamic imaging with worse statistics in short-frame data. To address the challenges, we incorporated anatomical information measured from higher resolution MRI in developing advanced functional image reconstruction techniques. For myocardial perfusion imaging, we developed dual motion correction techniques to minimize the effect of respiratory and cardiac motion on the task of defect detection. For dynamic cardiac imaging, we developed spatiotemporal direct parametric image reconstruction techniques to improve the estimation of myocardial blood flow. These developments advance ET imaging in quantitative measurement, which will bring more diagnostic and prognostic benefits into the care of patients with cancers, cardiovascular diseases, and brain disorders.