Flipping Hemisphere EEG Data


I have a cohort of stroke patients. Most are affected on their left hemisphere, but some on their right. For analysis, I would like to take left hemisphere as the “affected” side for every subject. As a naive approach, I could interchange the data with the corresponding contralateral electrode, say C3 == C4 and viceversa for right-affected strokes. Will this have serious consequences on the interpretation of the results? Is there another more common approach? In the case of source space, maybe I can try projecting the signals to fsaverage_sym?

I know that the questions are very broad, but I appreaciate any advice that leads me in the right direction.