I am not certain what you want to do.
If you want to get the peaks and their indices, request those outputs:
[pks,locs] = findpeaks(pure_brain(:,2));
I have no idea what is in your data file, however if you want to plot them and indicate them, try this:
x = 1:size(pure_brain,1);
plot(x(locs), pure_brain(locs,2), '^r')