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Erin, Yes I think that this would explain what you are seeing. The % calculation assumes that both COPE1 and COPE5 have the same units, if there has been a rescaling then they won't match any more - so it looks like you should also include the PPHeights in the calculation. Micahel On 9 Apr 2013, at 21:10, Erin Mazerolle <[log in to unmask]> wrote: > Hi Michael, > > 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, > Erin >