Hi Sungshin,
We refer to those 2 pairs of distortion correction images as forward and reverse blip datasets. The forward direction should match that of the functional EPI data, while the reverse is the opposite.
Those 2 datasets can be passed to afni_proc.py using -blip options:
-blip_forward_dset FORWARD+orig \
-blip_reverse_dset REVERSE+orig \
The resulting proc script will have a 'blip' processing block, which you are welcomed to review.
There is no option to apply per-run reference images (except to pre-process using multiple afni_proc.py commands). If shimmimg was applied between runs, it would be a good idea to use per-run registration. Otherwise, it is unlikely to matter much.
- rick
