A method of engaging a medical instrument with a medical instrument manipulator comprises receiving an indication that a first input coupling of the medical instrument is positioned adjacent to a first drive output of the manipulator. The first drive output is driven by a first actuating element. In response to receiving the indication, the first drive output is rotated in a first rotational direction. A determination is made, by one or more processors, as to whether a resistance torque is experienced by the first actuating element after rotating the first drive output in the first rotational direction. If the resistance torque is not experienced by the first actuating element after rotating of the first drive output in the first rotational direction, the first drive output is rotated in a second rotational direction. A determination is made, by the one or more processors, as to whether a resistance torque is experienced by the first actuating element after rotating of the first drive output in the second rotational direction.