We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
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.