A main advantage of PET is that it provides quantitative measures of the radiotracer concentration, but its accuracy is confounded by several factors, including attenuation, subject motion, and limited spatial resolution. Using the information from one simultaneously acquired morphological MR sequence with embedded navigators, we propose an efficient method called MR-assisted PET data optimization (MaPET) to perform attenuation correction (AC), motion correction, and anatomy-aided reconstruction. Methods: For attenuation correction, voxel-wise linear attenuation coefficient maps were generated using an SPM8-based approach method on the MR volume. The embedded navigators were used to derive head motion estimates for event-based PET motion correction. The anatomy provided by the MR volume was incorporated into the PET image reconstruction using a kernel-based method. Region-based analyses were carried out to assess the quality of images generated through various stages of PET data optimization. Results: The optimized PET images reconstructed with MaPET was superior in image quality compared to images reconstructed using only attenuation correction, with high SNR and low coefficient of variation (5.08 and 0.229 in a composite cortical region compared to 3.12 and 0.570). The optimized images were also shown using the Cohen's d metric to achieve a greater effect size in distinguishing cortical regions with hypometabolism from regions of preserved metabolism in each individual for different diagnosis groups. Conclusion: We have shown the spatiotemporally correlated data acquired using a single MR sequence can be used for PET attenuation, motion and partial volume effects corrections and the MaPET method may enable more accurate assessment of pathological changes in dementia and other brain disorders.