Dear Nina,
With only two trials a session it is somewhat questionable whether you should rely on these estimates at all, as it might indicate something trivial (e.g. the subject didn't understand the task during that run at all). Weighting according to the no. of trials might also become problematic for differential contrasts, e.g. something like 10, 10, 1, 1 trials for conditions A1-4 and 1, 1, 10, 10 for conditions B1-4. The runs would contribute to a different extent for different conditions then, and this might introduce a bias (A vs. B resembles A1+A2 vs. B3+B4).
Best
Helmut
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