Dear Joelle,
> In essence, I could actually just look at the first part of each trial.
Well, the question is whether a homogeneous (and once it's established, constant) activation pattern throughout the long trial is a good assumption or not. As you stated it's some learning paradigm, if there were e.g. a learning part and a recall part within a trial, then the assumption would probably be bad, which would usually result in underestimating the activations.
Best
Helmut
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