Most of the studies employing neuroimaging have focused on cortical and subcortical signals individually to obtain neurophysiological signatures of cognitive functions. However, understanding the dynamic communication between the cortex and subcortical structures is essential for unraveling the neural correlates of cognition. In this quest, magnetoencephalography (MEG) and electroencephalography (EEG) are the methods of choice because they are non-invasive electrophysiological recording techniques with high temporal resolution. Sophisticated MEG/EEG source estimation techniques and network analysis methods developed recently can provide a more comprehensive understanding of the neurophysiological mechanisms of fundamental cognitive processes. Used together with non-invasive modulation of cortical-subcortical communication, these approaches may open up new possibilities for expanding the repertoire of non-invasive cognitive neurotechnology.