A system example may include electrodes operationally positioned for use in delivering sub-perception neural modulation, a neural modulator configured to use at least some electrodes to generate a modulation field, and a feedback system configured to receive a feedback signal that a generated modulation field provides a perceived or measurable response. A control system may implement a calibration process including controlling the neural modulator to generate the modulation field using a first and second stimulus pulse with a first and second pulse width, respectively, and using the feedback system to determine a first and second reference point that represents an intensity of the modulation field generated using the first and second pulse widths, respectively, that provides the response, and deriving sub-perception calibration data specific to sub-perception modulation delivered using a sub-perception pulse with a sub-perception pulse width.
