Hi Peter,
Have you seen this thread?
If there is an effect of disease on the response functions, I’d guess its effect will be small. You can always run dwi2response on all data and compare response functions across groups to verify this (shview, or via plotting of the numerical values). If response functions genuinely are different, you’d still need to decide on a common set of response functions so that your ODFs are directly comparable. For interpretation reasons, I’d use the response functions from the control group. If abnormal single fibre WM in AD brains looks genuinely different, you’d see the effect in the ODFs (unless the non-negativity constraint or multi-shell signal signature prevent this).