afni_proc.py was created by Rick Reynolds in 2006 (yeeeees, way back then), but never had a full "methods paper" introduction to the world. Until this week!
Please see here for the an initial draft and description:
It is complemented by this draft describing some QC features in AFNI generally and several in afni_proc.py specifically:
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Just stumbled upon this announcement reading the automated summary from the message board. This is a very useful resource to share with anyone getting into fMRI data processing. I've always appreciated the elaborate examples on the -help page of afni_proc but this paper would have saved me countless hours of googling specific options, coming from a non-technical background. Thanks for taking the time to put this together! :)
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I'm glad that this was useful. We try to cover a lot of scenarios, though there are many more still. And indeed, it is pretty overdue---it has been on our 'to do' list for a while.
But don't worry, we're still happy to discuss any processing questions that come up, of course, on the Message Board.
I will also take the opportunity to point readers to additional examples of AFNI processing that goes along with publications/posters/etc., in what we call the AFNI Codex (= Code Examples). Many of these include afni_proc.py commands with comments in the code and/or paper about what options were used and why. (And you might recognize some of the contributing authors!)
--pt