This is mouse fMRI, and the slice selection is done axially - meaning that the slices are coronal (not horizontal). this is due to the mouse brain not being bent at 90° in the middle (as e.g. the human brain is).
We should definitely try disabling the time realignment; I was unaware that this can be done by omitting inputs. However, since our mice are well fixed and anesthetized, spatial realignment is of less concern to us than slice timing correction. So we definitely want to be able to do slice timing correction (preferably via a python tool) - it's spatial realignment which we could forego.
Not least of all, our stimulus evoked activation is quite strong, and spread across much of the cortex. I was afraid, that it might get categorized and filtered out as "motion" - do you know if SpaceTimeRealign does motion correction behind the scenes? We had trouble actually understanding the code.