Thanks for your reply. I think I figured out where I might have been going wrong. Is it possible that 100*COPE1/COPE5 will only work if your PPHeights are approximately the same for both PE1 (control-tag baseline) and PE3 (perfusion activation)? Otherwise, will we need to scale by PPHeights (or baseline/max range), rather than use the raw copes?
I was using a sine basis function convolution for my perfusion activation parameter, and getting PPheight of ~750 (versus a PPheight of 1 for my control-tag baseline parameter).
Does this sound sensible, or have I just happened upon a factor that gives me percent signal change in a more reasonable range for perfusion data (whereas with the raw cope values my percent signal change results are ~0.06% (versus ~48% when I multiply cope1 by the PPheight first).
Thanks again for the clarification,