Aim: The research aimed to study and model the emotion-related activity of functional networks within the human brain cortex using power spectrum density and detrended phase transfer entropy methods. Attention was focused on revealing alterations in cognitive mechanisms, caused by presentation of neutral human faces as rare stimuli among faces with either negative or positive expression. Methods: EEG-data was recorded during the perception and processing of neutral human facial expressions, presented among positive and negative faces in two series of images, alongside with resting state with open and closed eyes, which was further analyzed using power spectrum density and detrended phase transfer entropy methods. Results: Specific EEG-bands (θ and β) were chosen for the analysis based on their prominent role in memory- and emotion-related mechanisms. The topography of the spectral power density corresponded to the generally accepted ideas describing perception and visual stimuli processing mechanisms. The phase transfer entropy method was not sufficient to analyze resting state data. The results of the analysis performed using the phase transfer entropy method revealed the problems of neutral faces differentiation when presented in a positive emotional context. Simultaneously, enhanced processes of motivational coding and self-reflection were observed during the presentation of neutral faces in a negative emotional context. These results corresponded with the data obtained in our previous ERP-based study. Conclusions: Phase transfer entropy and spectral power density have demonstrated their effectiveness in analyzing the mechanisms of emotional visual stimuli processing mediated in different cortical areas.