How to use "that is"?
It is acceptable to employ a comma before that is; but I would prefer a stronger disjunction, either a colon or a dash, simply to make the structure of this long sentence clearer. A comma after that is is conventional.
You do need to restructure the clause following that is as an indicative rather than an interrogative: that is, as "the reaction time to a given stimulus will show a decreased latency."