A medical procedure system, including a medical instrument to be inserted into a body part, and including position-tracking transducers to provide position signals, a distal end, and at least one radiopaque marker, a position tracking sub-system to compute a position including at least one location and orientation of the distal end in a position-tracking sub-system coordinate frame responsively to the position signals, a fluoroscope to capture fluoroscopic images of an interior of the body part and the radiopaque marker(s), and a registration sub-system to render, to a display, the captured fluoroscopic images including at least one marker-image of the radiopaque marker(s), and at least one graphical representation indicative of the computed position of the distal end, receive user-alignment input aligning the graphical representation(s) with the marker-image(s), and register the position-tracking sub-system coordinate frame with a coordinate frame of the fluoroscope responsively to the received user-alignment input.