A fitting algorithm for a spinal cord stimulator is disclosed, which is preferably implemented in a clinician programmer having a graphical user interface. In one example, coupling parameters indicative of coupling to neural structures are determined for each electrode in an implanted electrode array. The user interface associates different pole configurations with different anatomical targets and with different measurement techniques (subjective or objective) to gauge the effectiveness of the pole configuration at different positions in the electrode array. The pole configuration, perhaps as modified by the coupling parameters, is then steered in the array, and effectiveness is measured along with a paresthesia threshold at each position. Using at least this data, the fitting algorithm can determine one or more candidate positions in the electrode array at which a therapeutic stimulation program can be centered.
