Some comment about the reference slice: As far as I remember you have to enter the number of the slice as it was acquired on the scanner, not its position inside the acquisition scheme.
So with an acquisition order of 2:2:24 1:2:23 you would have to enter "24" or "1" as reference slice in case you want to correct onto the middle of the scan, not "12" or more generally, (number of slices)/2.
If you use slice timing, don't forget to set the microtime onset to (number of time bins)/2, so with 16 time bins (default value) you would use a microtime onset of 8 (or 9) during single-subject model specification.
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