Hi Leah,
The reason we have pushed Fourier interpolation out of much of
the processing is that while it can do very well with most data,
spikes end up producing ringing artifacts. For example, a motion
related spike (or any other spike) in some voxel's time series can
ring out through the rest of the time series (via 3dTshift), just
like spacial signals can produce ringing artifacts in the volume
(via 3dvolreg or 3dmerge).
So afni_proc.py defaults to avoiding Fourier, where it can.
- rick