System for navigating a surgical instrument

A method for determining a virtual position of a surgical instrument with respect to a three dimensional (3D) medical image, comprising:

• obtaining a first 3D medical image of a first volume of a patient's body, said first volume comprising a reference marker attached to the patient's body, the reference marker being configured to be localized by a tracking system,
• registering the first 3D medical image with said reference marker using fiducials of the reference marker visible in the first 3D medical image to determine a first transformation matrix,
• obtaining a second 3D medical image of a second volume of the patient's body, said second volume being different from the first volume and not containing all the fiducials of the reference marker, said first and second 3D images being obtained by a single imaging device, the imaging device being distinct from the tracking system,
• registering the second 3D medical image with the first 3D medical image to determine a second transformation matrix,
• localizing the surgical instrument with the tracking system,
• obtaining a virtual position of the surgical instrument with respect to the reference marker from the tracking system by determining a third transformation matrix,
• determining a virtual position of the surgical instrument with respect to the second 3D medical image based on the first, second and third transformation matrices.