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In this study we estimated time-varying cortical connectivity patterns 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 by using time-varying partial directed coherence. Connectivity was estimated from high resolution EEG recordings with the use of realistic head modelling and the linear inverse estimation of the cortical activity in a series of regions of interest of the cortex (ROIs). The experimental evidences obtained support the conclusion that the SCI population involved a larger cortical network than those generated by the healthy subjects during the task performance. Such 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. Such details about the temporal evolution of the connectivity patterns cannot be obtained with the application of the standard estimators of connectivity.