Methods and systems for obtaining and analyzing electromyography responses of electrodes of an implanted neurostimulation lead for use neurostimulation programming are provided herein. System setups for neural localization and/or programming include a clinician programmer coupleable with a temporary or permanent lead implantable in a patient and at least one pair of EMG sensing electrodes minimally invasively positioned on a skin surface or within the patient. The clinician programmer is configured to determine a plurality of recommended electrode configurations based on thresholds and EMG responses of the plurality of electrodes and rank the electrode configuration according to pre-determined criteria. The clinician programmer further includes graphical user interface on which the plurality of recommended electrode configurations are displayed for modification and/or selection by a clinician in programming an IPG or EPG coupled with the lead to apply a neurostimulation treatment according to the selected electrode configuration.