The technical difficulties associated with an active reference signal are now well recognized, i.e., the reference signal may contaminate EEG recordings and confound the interpretation of coherence analysis [29], [33], [34] and phase-synchrony analysis [22], [32], [35]. In order to correctly interpret commonly used metrics of neuronal synchrony in EEG, it is clearly necessary to identify the reference signal and its contribution. In [1], we proposed two methods to extract the scalp reference signal from multiple-channel iEEG recordings based on independent component analysis under the assumption that the reference signal from the scalp reference electrode can be treated as independent from all of the sources recorded at each intracranial electrode. This assumption is basically true because the reference scalp electrode is relatively isolated from the intracranial electrodes by the three intervening layers of cerebrospinal fluid, bone, and scalp. This assumption was supported by simulation results from clinical EEG data. In this study, we examined the effect of recording reference on commonly used quantitative methods for measuring neuronal synchrony. Using analytical methods, simulations, and experimental results from a patient with intracranial
