The invention relates to a system for navigating a surgical instrument (1), comprising a processor configured for:obtaining a first 3D medical image of a first volume (V1) of a patients body, said first volume (V1) comprising a reference marker (M),registering the first 3D image with said reference marker (M),obtaining a second 3D medical image of a second volume (V2) of the patients body, said second volume (V2) being different from the first volume (V1) and not containing the reference marker (M) in its entirety, said first and second 3D images being obtained by a single imaging device,registering the second 3D medical image with the first 3D medical image,obtaining a virtual position of the surgical instrument (1) with respect to the reference marker (M) from a tracking system,determining a virtual position of the surgical instrument (1) with respect to the second 3D medical image.
