Hi,
It might be worth pointing out that afni_proc.py will
actually run align_epi_anat.py for you if the 'align'
processing block is included. See example 6 and later
in the -help output:
afni_proc.py -help
Getting to your questions...
The base volume should be the same as the base volume
used in EPI alignment (3dvolreg). Otherwise, 3dvolreg
might undo the gain from align_epi_anat.py.
This has little to do with slice timing, which aligns
to a time within a TR, or maybe to a slice time within
the times from a volume. There is no volume chosen for
slice timing correction, but rather a slice.
- rick
