In the paper, we propose a simple algorithm that improves the quality with which the displacements between images registered in the sub-apertures of a a Shack-Hartmann (SH) wavefront sensor can be determined. Instead of measuring shifts between a given sub-aperture and a reference image, the method transforms a matrix of all relative displacements between sub-apertures into a vector of final shifts estimated with significantly increased accuracy. The method can be applied to any observations employing an SH wavefront sensor, especially if a scene evolves rapidly and a reference, high-fidelity image cannot be obtained. The proposed technique allows for reducing nonlinearities and biasing of estimations present in current state of the art methods.