A recently-submitted bioRxiv draft (not by AFNI authors) described “default FMRI processing” using various softwares, including AFNI. In further dialogue with this work, we comment on many of the steps chosen therein with AFNI, and provide several recommendations in the forms of both code snippets and philosophical musings. The AFNI draft is located on bioRxiv:
https://www.biorxiv.org/content/early/2018/04/28/308643
There are also some of the associated codes are located here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/codex/fmri_detailed.html
(Please note that while some those codes do contain fixes from the other paper and recommended steps in analyzing FMRI data, there are still several cases where things we would not recommend were left in the codes, for the purposes of comparison with the other authors’ text; please refer to our bioRxiv comments for details.)
Glancing through the AFNI draft might be useful, as it discusses several points related to FMRI processing in general and with afni_proc.py in particular.
–pt