A method for selecting data to reconstruct a three-dimensional (3D) image of a subject of interest includes acquiring a 3D emission dataset of the subject of interest, acquiring a respiratory signal of the subject of interest, the respiratory signal including a plurality of respiratory cycles, and calculating a respiratory profile using the respiratory signal. The method further includes, for each respiratory cycle, generating a gating window, calculating a minimum total squared difference (TSD) between a plurality of phases in the respiratory profile and the same plurality of phases in the respiratory cycle, and positioning the gating window based on the TSD values calculated, and reconstructing a 3D image using only the emission data within the plurality of gated windows. A system and non-transitory computer readable medium are also described herein.