Dear Jindra,
Changing the microtime onset means you shift the predictors in time relative to the data (+/- TR/2 in your case). Depending on setting you thus predict peaks "too early" or "too late", or from a different perspective, you optimize your predictors towards trial components that occur at an earlier or at a later point. This should indeed have rather strong effects in an event-related design like yours.
In general one would want to set the microtime onset to that point in time which you chose as a reference during slice timing, usually the slice acquired in the middle of the TR. In your case, you would thus usually go with 2 or 47 as a reference slice during slice timing, and for the microtime onset e.g. the 23rd time bin out of 47 time bins. You don't have to go with 23 and 47 though (it's just very simple to define the "middle" in that case), you could also go with the default setting 8 and 16 (also the middle) or 1000 and 2000. See a previous message at https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;53708327.1508
By the way, if there were motion artefacts then changing the microtime settings does not help (although it might be the case that in one instance, they are "more visible").
Best
Helmut
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