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Objective:In this paper, we propose a body of techniques for the estimation of rapidly changing connectivity relationships between EEG signals estimated in cortical areas, based on the use of adaptive multivariate autoregressive modeling (AMVAR) for the estimation of a time-varying partial directed coherence (PDC). This approach allows the observation of rapidly changing influences between the cortical areas during the execution of a task, and does not require the stationarity of the signals. Methods:High resolution EEG data were recorded from a group of spinal cord injured (SCI) patients during the attempt to move a paralyzed limb. These data were compared with the time-varying connectivity patterns estimated in a control group during the real execution of the movement. Connectivity was estimated with the use of realistic head modeling and the linear inverse estimation of the cortical activity in a series of regions of interest by using time-varying PDC. Results:The SCI population involved a different cortical network than those generated by the healthy subjects during the task performance. Such a network differs for the involvement of the parietal cortices, which increases in strength near to the movement imagination onset for the SCI when compared to the normal population. Conclusions:The application of time-varying PDC allows tracking the evolution of the connectivity between cortical areas in the analyzed populations during the proposed tasks. Such details about the temporal evolution of the connectivity patterns estimated cannot be obtained with the application of the standard estimators of connectivity.