Recent studies have demonstrated the efficacy of brain-machine interfaces (BMI) for motor rehabilitation after stroke, especially for those patients with severe paralysis. However, a cerebro-vascular accident can affect the brain in many different manners, and lesions in diverse areas, even from significantly different volumes, can lead to similar or equal motor deficits. The location of the insult influences the way the brain activates when moving or attempting to move a paralyzed limb. Since the essence of a rehabilitative BMI is to precisely decode motor commands from the brain, it is crucial to characterize how lesion location affects the measured signals and if and how it influences BMI performance. This paper compares the performances of an electroencephalography (EEG)-based movement intention decoder in two groups of severely paralyzed chronic stroke patients: 14 with subcortical lesions and 14 with mixed (i.e., cortical and subcortical) lesions. We show that the lesion location influences the performance of the BMI when decoding the movement attempts of the paretic arm. The obtained results underline the need for further developments for a better individualization of BMI-based rehabilitative therapies for stroke patients.