In human psychophysics this control is typically obtained through instruction, perhaps bought with some material reward. In animal experiments one uses such facts as that water deprivation typically motivates the animal to try to maximise its uptake of liquid. As an experimenter one needs to have some notion of the affordances of the stimuli, otherwise psychophysics becomes impossible and all that is left to do is to practice physiology. The observer behaves in a certain way because it has seen certain things, and knows that the behaviour is likely to bring certain results about because it has seen these things. But notice that our conclusion that the observer behaves in a certain way because it has seen certain things, and knows that the behaviour is likely to bring certain results about because it has seen these things, doesn't depend in the least on how brain scans would look when collected during the process.
Brain activity is at most part of mere particular action of the observer.
Thus, such data simply don't bear on the conclusion at all. Brain scanning and psychophysics are independent endeavours. Neurophysiology reveals causal connections between brain states. Psychophysics reveals the structure of perceptions. One conceptually switches to psychophysics , in the most simplistic case implicitly replacing the pushing of a button with the firing of an axon, say.