The phase difference method of phase contrast MR angiography provides a means of measuring the average velocity in each voxel of an MR scan. When static tissue is present in a voxel containing flow, the measured velocity is not the average velocity of the flow alone, but is lower due to the partial volume effect of the static tissue. We present a preprocessing technique that removes the contribution of static tissue in each voxel prior to calculation of average velocity, resulting in more accurate velocity measurements and better lumen definition. Results of flow tube experiments are presented which confirm the improvement in measurement accuracy.