Hi Noah,

Just to add a bit to Paul's useful suggestions...

To find help for "all" of the AFNI programs, consider
all program help.

If you want to regress out ventricles and white
matter signals, then "Example 11" from the help
of afni_proc.py is the place to start. Note that
it does not use bandpassing, if you care.

Note that there is no "best" method. Not anywhere.
We only do what seems reasonable.

Example 11 includes passing masks for the ventricles
and white matter, and the top 3 principal components
from ventricles are regressed out, along with using
ANATICOR and the average white matter signal (maybe
that is redundant?).

This example assumes that you have such masks in
alignment with the anatomical dataset (perhaps they
are all output from FreeSurfer). It also uses
non-linear registration to the anatomical template.

For the most part, the work in using this example
is in creating the masks. For example, the ventricles
can come from ROIs 4 and 43 from the segmentation
dataset.

- rick