1. A method, comprising: controlling a first modality unit and a second modality unit to perform a plurality of scans, including a first scan with the first modality unit and the second modality unit and a second scan with the first modality unit and the second modality unit, of an object, wherein the object is positioned in a first orientation during the first scan and a second orientation during the second scan, wherein the first modality unit and the second modality unit respectively comprise a positron emission tomography (PET) imaging system and a computed tomography (CT) imaging system; calculating a plurality of alignment parameters of the first modality unit and the second modality unit based on images reconstructed from data acquired during the plurality of scans; and adjusting alignment of the first modality unit and the second modality unit based on the plurality of alignment parameters.