I'd still worry that if the TR is different, there could be bias even if the peristimulus sampling times are similar, because of MRI physics issues. I don't know enough MRI physics to say that for sure, just that if the TR is different, I'd assume the statistical nature of the EPI could be different. Whether and how that would work itself into bias at the level of a contrast I can't say---someone with more knowledge would have to chime in. Sounds like maybe not if you didn't find any differences in control conditions, though since this is a subtle issue one would have to look very carefully at the details.
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