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Abstract: Objective: Computer-aided-surgery in ENT surgery is mainly used for sinus surgery but navigation accuracy still reaches its limits for skull base procedures. Knowledge of navigation accuracy in distinct anatomical regions is therefore mandatory. This study examined whether navigation accuracy can be improved in specific anatomical localizations by using hybrid registration technique.<br><br>Study design: Experimental phantom study.<br><br>Setting: Operating room.<br><br>Subjects and methods: The gold standard of screw registration was compared with automatic LED-mask-registration alone, and in combination with additional surface matching. 3D-printer-based skull models with individual fabricated silicone skin were used for the experiments. Overall navigation accuracy considering 26 target fiducials distributed over each skull was measured as well as the accuracy on selected anatomic localizations.<br><br>Results: Overall navigation accuracy was 1.0 mm in all cases, showing the significantly lowest values after screw registration (0.66 ± 0.08 mm), followed by hybrid registration (0.83± 0.08 mm), and sole mask registration (0.92 ± 0.13 mm).On selected anatomic localizations screw registration was significantly superior on the sphenoid sinus and on the internal auditory canal. However, mask registration showed significantly better accuracy results on the midface. Navigation accuracy on skull base localizations could be significantly improved by the combination of mask registration and additional surface matching.br