A method and apparatus for imaging within the eye is provided whereby a component of eye position is detected using optical imaging data. Tracking eye position over time and correctly registering imaging data for scan locations or using eye position to detect decentration achieves improved imaging. In one embodiment, essentially perpendicular B-scans are imaged sequentially and the corneal arc within each B-scan is analyzed to determine the vertex of the eye. The eye vertex is tracked over pairs of perpendicular B-scans to determine eye motion. In another embodiment, the decentration in the Pachymetry map is removed by correcting for the misalignment of the center of the Pachymetry map and the actual location of the corneal vertex.