Hi Aditya,

Actually, we recommend despiking as the first step, if it is
done at all. Temporal alignment of slices would be done next
(if the TR isn't too big), followed volume registration. That
is the default order of those steps if afni_proc.py is used to
generate the processing script.

Note that by default, afni_proc.py does not do despiking.

Working backwards, we tend to suggest time shifting before volume
registration, since registration seems to mess up timing more than
time shifting messes up registration. And we tend to suggest
despiking before time shifting, so that the spikes are not blurred
over time.

- rick