> 1) the activity associated with the stimulus presentation;
> 2) the activity associated with the motor response.

Is the reason you have a 2 x 2 structure because each of the two stimulus presentations is associated with one motor response?

> - It is a 2x2 factorial paradigm, so there are 4 conditions.

If you consider those 4 conditions as a 2 x 2 structure, then it's a two-way within-subject (or repeated-measures) ANOVA, which can be directly handled by 3dANOVA3 -type 4. Of course, you can also use 3dMVM, but it would take much longer runtime.

Unless it's not really a 2 x 2 factorial structure.

Gang