Misalignment of PET and CT images can occur at the diaphragm due to respiratory motion and movement of internal organs above and below the diaphragm. Because the PET scan is acquired over several minutes with the patient tidal breathing, the structures at the diaphragm undergo slight blurring or smearing. The contour of the diaphragm therefore appears in the neutral position. If the patient were to be in deep inspiration during the CT acquisition, the organs around the diaphragm would be in a different position from that in the emission PET scan. This misalignment can cause attenuation correction artifacts. The liver dome and spleen may be seen 'floating' above the diaphragm.

Possible limitations:
Hypermetabolic foci in the dome of the liver can be falsely localized in the lung base on attenuation corrected images. This is important to avoid misdiagnosis of disease in the lung base. This is especially important in a patient with lower lung nodules that are not metabolically hyperactive.