Method and system for operating a surgical instrument

A system comprising:

• a manually operated instrument including a lumen;
• a reference fixture positioned in a fixed world reference frame and coupled to a proximal portion of the manually operated instrument;
• an interrogator, wherein the reference fixture is movable relative to the interrogator in the fixed world reference frame;
• a shape sensor coupled to the manually operated instrument and extending through the lumen of the manually operated instrument, the lumen being rotatable relative to the shape sensor about a longitudinal axis of the lumen, the shape sensor further extending from the manually operated instrument to the reference fixture, the shape sensor further extending through the reference fixture and to the interrogator such that a portion of the shape sensor extends between the reference fixture and the interrogator;
• and
• a controller configured to:
• receive, from the shape sensor, shape information for the manually operated instrument;
• and
• determine a pose of the manually operated instrument in the fixed world reference frame based on the shape information for the manually operated instrument.