PURPOSE: Clinical whole-body (WB) PET images can be compensated for respiratory motion using data-driven gating (DDG). However, PET DDG images may still exhibit motion artefacts at the diaphragm if the CT is acquired in a different respiratory phase than the PET image. This study evaluates the combined use of PET DDG and a deep-learning model (AIR-PETCT) for elastic registration of CT (WarpCT) to the non attenuation- and non scatter-corrected PET image (PET NAC), enabling improved PET reconstruction. METHODS: The validation cohort included 20 patients referred for clinical FDG PET/CT, undergoing two CT scans: a free respiration CT RESULTS: AIR-PETCT was robust and generated consistent WarpCTs when registering different CTs to the same PET NAC. The use of WarpCT instead of CT consistently led to equivalent or improved PET image quality. The algorithm significantly reduced "banana" artefacts and improved lesion-to-background ratios around the diaphragm. The blinded clinicians clearly preferred PET DDG images reconstructed using WarpCT. CONCLUSION: AIR-PETCT effectively reduces respiratory motion artefacts from PET images, while improving lesion contrast. The combination of PET DDG and WarpCT holds promise for clinical application, improving PET image evaluation and diagnostic confidence.