Dear Haleh,
jitter is used to sample your hemodynamic response at different times after each stimulus. There is no need to align your reference slice or time bin to a particular event type.
Your choice of microtime onset will instead depend on your reference slice for slice timing (if you did that). Also, you may need to adjust your stimulus onsets to match slice timing and microtime onset choices. There are many pros and cons for each setting. If unsure, try with the defaults (1st slice and 1st time bin) before doing something else.
Hope this helps,
Volkmar
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