In my nipype pipeline, I'm using SPM's slice timing correction tool and I'm trying to find out whether I need to adjust my event onsets in the first-level design matrix or whether this is automatically updated. For example, in a continuous paradigm if my TR=2, and my reference slice is the middle slice, then it is as if all of my acquisitions occur at Time=1s, 3s, 5s, etc. instead of Time = 0s, 2s, 4s, etc. Because the design matrix sets Time=0 to align with the first acquisition (which was corrected to align with Time=1s), then theoretically I would have to shift all of my event onsets back by 1 second to make sure the expected HRF is modeled correctly.
Does this get accounted for automatically in SPM (or any other software) or do I need to adjust all of my event onset times? You would think since this applies to any event-related protocol it would be widely discussed, but I can't find any mention of this necessity on the internet or in SPM's manual...