I would like to use unWarpEPI.py to perform correction with opposite polarity data (blip-down). I was wondering why in the help of afni_proc.py it is recommended to use this program after tshift, and also where correction with retroicor should be placed in this context, whether before or after unwarping.
The steps are implemented directly in afnI_proc.py, it does not
use unWarpEPI.py. To have AP.py do the unwarping, pass the
forward and reverse direction datasets via:
The FORWARD dastaset should match the direction of the
main EPI data, used in the analysis.