Instrument presence and rotational offset sensing in flexible system

At least one non-transitory computer-readable medium comprising instructions thereon that, when executed by at least one processor associated with a medical system, the medical system comprising an elongated flexible body including a channel extending through the elongated flexible body, wherein the elongated flexible body includes an articulable portion extending along at least a portion of a length of the elongated flexible body, and an instrument configured to be received in the channel of the elongated flexible body, cause the medical system to:

• receive sensor data from a magnetic field sensor, the sensor data indicative of a magnetic field at the magnetic field sensor, wherein the magnetic field is generated by a magnetic field generator;
• and
• based on the sensor data, determine a relative rotational orientation between the elongated flexible body and the instrument within the channel,
• wherein the magnetic field generator and the magnetic field sensor are in one selected from a group consisting of a first arrangement and a second arrangement,
• wherein in the first arrangement:
• the magnetic field generator is attached to the elongated flexible body, and the magnetic field sensor is attached to the instrument, and
• rotation of the instrument with respect to the elongated flexible body causes the magnetic field sensor attached to the instrument to rotate with respect to the magnetic field generator attached to the instrument, and
• wherein in the second arrangement:
• the magnetic field generator is attached to the instrument, and the magnetic field sensor is attached to the elongated flexible body, and
• rotation of the instrument with respect to the elongated flexible body causes the magnetic field generator attached to the instrument to rotate with respect to the magnetic field sensor attached to the elongated flexible body.