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In the interest of stimulating discussion, I guess I'll respond, and 
throw some suggestions out there. Hopefully the experts will reply...

I think if you properly design your experiment, ensuring a range of 
SOA's, you can still estimate the contribution of each condition 
(assuming linearity). See e.g. Miezin et al. 2000 NeuroImage, Fig. 1. 
But, for SOAs below 2000ms linearity might not hold.
Maybe you could do something like in Ollinger et al 2001 NeuroImage... 
they separated components of trials.
If you're interested in varying the SOA and looking at its effect on 
activity, perhaps you could do some kind of parametric modulation?
Or maybe you can set up a factorial design, 2 x 2 (task A, task B; short 
SOA, long SOA)...

Andre Szameitat wrote:
> Dear SPMers,
> I've sent this question before but didn't receive an answer. However as
> this was directly before the Easter holidays so that not all may have
> read it and this question is quite important for me, I'd like to post it
> again:
>
> I have a question about a very specific situation, in which non-linear
> effects may occur (due to the refractoriness of the hemodynamic
> response, i.e. the second of two successive identical stimuli evokes a
> smaller and delayed BOLD response). However, in my view they cannot be
> corrected - but I would be happy if you prove me wrong :-)
>
> The situation is a dual-task situation: Suppose you have two tasks A
> and B, which are performed with varying temporal distance (stimulus
> onset asynchrony, SOA). In cognitive psychology, it has been argued that
> the shorter the SOA, the higher the demands on executive functions, e.g.
> related to the coordination of overlapping task processing. Thus, as a
> first effect, in a dual-task related brain area X we would expect
> increasing levels of activity with decreasing SOA.
>
> However, it is not uncommon that already the individual performance of
> each task activates such a dual-task related brain area as well. Thus,
> suppose task A performed alone activates area X, and task B performed
> alone activates area X as well. When we decrease the SOA to create a
> dual-task situation, then there should be non-linearities due to the
> hemodynamic refractoriness. This is particularly so because the time
> range of hemodynamic refractoriness and SOA manipulations in dual-task
> paradigms is identical (usuallly SOA varies between 0 and 1500/2000 ms).
> Thus, as a second effect, in a dual-task related brain area X we would
> expect decreasing levels of activity with decreasing SOA.
>
> Taken together, it appears to me that there are two perfectly
> confounded effects: Psychological processes predict an increase of
> activity with decreasing SOA, while non-linear BOLD effects predict a
> decrease of activity with decreasing SOA. Stated more generally, both
> effects result in a parallel (negatively correlated) modulation of the
> BOLD response. Therefore, it seems to me that such non-linear BOLD
> effects cannot be corrected. For instance, an additional regressor like
> the one added if Volterra kernels in SPM are used should be fully
> colinear with a regressor encoding the SOA (the psychological
> manipulation).
>
> It would be great if I am missing something and there would be a method
> that these two effects can be disentangled. Thus, any input is greatly
> appreciated.
>
> Kind Regards,
> Andre
>