Systems and methods for efficiently obtaining optical coherence tomography (OCT) measurement data with reduced effects of motion are presented. One embodiment of the present invention involves determining the amount of motion present during the collection of an OCT data set based on images of the eye collected at the same time as the OCT data and recollecting select portions of the OCT data set when the amount of eye motion is determined to exceed a predetermined threshold. Additional aspects of the invention include enabling or disabling the tracking feature in the system based on the quality of the images available for tracking and tracking based on an image collected during a prior examination of the patient to allow repeat scanning at the same location. A further embodiment of the invention includes reducing the effect of motion in the axial or z direction of the data based on a comparison to a model of the eye constructed from OCT data. The method can also be used to reduce the presence of mirror image artifacts in an OCT image.
