A medical instrument system comprising: a movement detector; a flexible catheter (104, 216, 310) having a proximal end couplable to an instrument carriage that is moveable along an insertion stage; a point gathering instrument extending along a length of the flexible catheter; and a tracking system configured to register a set of measured points collected by the point gathering instrument to a model of one or more anatomic passageways, wherein the tracking system performs operations comprising: accessing a set of model points of the model, the model points being associated with a model space; collecting the set of measured points along the length of the flexible catheter inserted into the one or more anatomic passageways of a patient, the measured points being determined by a shape of the catheter in a patient space; assigning the set of measured points into subsets according to a periodic physiological function monitored by the movement detector; selecting a first registration candidate from a plurality of registration candidates based on the subsets of measured points; applying the selected first registration candidate to the set of model points of the model to register the model to the patient space; characterised in that the tracking system further performs operations comprising: detecting a change in a comparison metric used to select the first registration candidate from the plurality of registration candidates; selecting a second registration candidate of the plurality of registration candidates based on the change in the comparison metric; applying the selected second registration candidate to register the model to the patient space; and altering the subset of measured points associated with the first registration candidate. a movement detector; a flexible catheter (104, 216, 310) having a proximal end couplable to an instrument carriage that is moveable along an insertion stage; a point gathering instrument extending along a length of the flexible catheter; and a tracking system configured to register a set of measured points collected by the point gathering instrument to a model of one or more anatomic passageways, wherein the tracking system performs operations comprising: accessing a set of model points of the model, the model points being associated with a model space; collecting the set of measured points along the length of the flexible catheter inserted into the one or more anatomic passageways of a patient, the measured points being determined by a shape of the catheter in a patient space; assigning the set of measured points into subsets according to a periodic physiological function monitored by the movement detector; selecting a first registration candidate from a plurality of registration candidates based on the subsets of measured points; applying the selected first registration candidate to the set of model points of the model to register the model to the patient space; characterised in that the tracking system further performs operations comprising: detecting a change in a comparison metric used to select the first registration candidate from the plurality of registration candidates; selecting a second registration candidate of the plurality of registration candidates based on the change in the comparison metric; applying the selected second registration candidate to register the model to the patient space; and altering the subset of measured points associated with the first registration candidate. accessing a set of model points of the model, the model points being associated with a model space; collecting the set of measured points along the length of the flexible catheter inserted into the one or more anatomic passageways of a patient, the measured points being determined by a shape of the catheter in a patient space; assigning the set of measured points into subsets according to a periodic physiological function monitored by the movement detector; selecting a first registration candidate from a plurality of registration candidates based on the subsets of measured points; applying the selected first registration candidate to the set of model points of the model to register the model to the patient space; characterised in that the tracking system further performs operations comprising: detecting a change in a comparison metric used to select the first registration candidate from the plurality of registration candidates; selecting a second registration candidate of the plurality of registration candidates based on the change in the comparison metric; applying the selected second registration candidate to register the model to the patient space; and altering the subset of measured points associated with the first registration candidate. detecting a change in a comparison metric used to select the first registration candidate from the plurality of registration candidates; selecting a second registration candidate of the plurality of registration candidates based on the change in the comparison metric; applying the selected second registration candidate to register the model to the patient space; and altering the subset of measured points associated with the first registration candidate.