afni.nimh.nih.gov

afni_proc.py is the program that will do all of this. It is able to call all of the other programs you mentioned. See the help for that program, paying particular attention to the examples that get progressively more complicated. We also have the AFNI academy videos (Start to Finish) and tutorials on afni_proc.py.

[www.youtube.com]
[afni.nimh.nih.gov]