Hi Rick,
Yes, that does make sense. I hadn't thought about the fact that slice time correction aligns everything to the start of the TR and that some slices would be finished before a stimulus occurring after the start of that final TR. I agree that it doesn't make much sense to present stimuli this late - I've never encountered this issue in previous fMRI work because we have always left the final TRs empty to avoid such issues, but the data I am currently working with were collected many years ago.
In any case, thank you for your insights. This really does help. I didn't want to lose those trials if they were actually valid, but now that I understand what is happening, I think it makes the most sense to allow 3dDeconvolve to run as is and leave out those few trials that started after the last TR. I don't think there is much to gain from trying to alter the slice times to include them if there would not be enough time for the BOLD response anyway.
Thanks!
Katelyn
