Resting-state fMRI (rs-fMRI) studies of the human brain have demonstrated that low-frequency fluctuations can define functionally relevant resting state networks (RSNs). The majority of these methods rely on Pearson's correlation for quantifying the functional connectivity between the time series from different regions. However, it is well-known that correlation is limited to quantifying only linear relationships between the time series and assumes stationarity of the underlying processes. Many empirical studies indicate nonstationarity of the BOLD signals. In this paper, we adapt a measure of time-varying phase synchrony to quantify the functional connectivity and modify it to distinguish between synchronization and desynchronization. The proposed measure is compared to the conventional Pearson's correlation method for rs-fMRI analyses on two subjects (six scans per subject) in terms of their reproducibility.