Dear Marek,
You're right, in case the regressors correspond to separate "conditions" and assuming you rely on the canonical HRF without derivatives then the order does not matter because there's no orthogonalization between condition regressors (there's orthogonalization within condition regressors though in case you work with derivatives or FIR sets). You can simply try out by changing the order when e.g. setting up the design matrix via the GUI. This would also be the easiest way if you really wanted to change the order (e.g. for having the relevant ones at the beginning to be able to go with "short" contrast vectors, as the other columns are zero-padded automatically). The raw design matrix is stored in xX.X, the filtered and whitened one in xX.xKXs.X.
The order *does* matter when working with parametric modulators, as the PMs of a certain condition undergo serial orthogonalization (in case the orthogonalization is turned on; the GUI in SPM12 has a corresponding option which was not present in previous versions). The first PM regressor would explain variance unexplained by the condition regressor then, the second PM regressor would explain variance unexplained by the condition regressor and the first PM regressor and so on.
But leaving this aside, what do you try to model with the arousal / valence regressors exactly, something like the button presses and/or the response window? This should be okay. In case you're aiming at capturing the within-condition variance of your different stimulus responses reflected by your different condition regressors then you would have to go with two parametric modulators for each of the condition regressors. Whether to go with serial orthogonalization is another issue then. One could also think of a set of regressors in which the arousal and valence "PMs" are "only" mean-centered with regard to their condition regressor (this way avoiding the problem with valence being orthogonalized with respect to arousal or vice versa). This doesn't work with the GUI though.
Maybe you can provide some more information on the design to clarify this aspect; possibly this was also why the reviewer asked for modifications.
Best
Helmut
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