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Non-invasive brain-computer interfaces (BCIs) can translate bioelectric signals collected via EEG into output computer commands (Wolpaw, 2007). In the recent years, BCIs have been used for neurorehabilitation of motor deficits (Page, Levine, Leonard, 2007). Integration of a motor-imagery BCI with functional electrical stimulation (FES) feedback might prove to be an effective tool for inducing beneficial plastic changes for neurorehabilitation. It has been shown that short-term plasticity can be measured by event related desynchronization (ERD) – which corresponds to the activation of sensorimotor areas of the brain, and by changes in MEP amplitudes (elicited via TMS), which signify of the level of corticospinal excitability (Pfurtscheller, 2001; Sauseng et al., 2009). Here we propose a plan to evaluate the hypothesis that trainings with a BCI-FES system modulate the sensorimotor activity of the human brain as evaluated through combined EEG-TMS methodology . The purpose of this study will be to provide preliminary evidence that such a system will be beneficial for post-stroke neurorehabilitation of motor deficits and can be further developed in the clinical setting as the next step of this research.