Patient movements during the acquisition of SD-OCT scans create substantial motion artefacts in the volumetric data that hinder registration and 3D analysis and can be mistaken for pathologies. In this paper we propose a method to correct these artefacts using a single volume scan while still retaining the overall shape of the retina. The method was quantitatively validated using a set of synthetic SD-OCT volumes and qualitatively by a group of trained OCT grading experts on 100 SD-OCT scans. Furthermore, we compared the motion compensation estimation by the proposed method with a hardware eye tracker on 100 SD-OCT volumes.