Hi Brian,

Assuming that you want to just apply them as additional
regressors (which means they are TR-locked and match
your EPI data), then you would need to add them to the
3dDeconvolve command in the afni_proc.py processing
script.

Note that afni_proc.py does not (currently) have a way
to add extra regressors (assuming you are using the
-regress_stim_times option). That is something I should
add.

In any case, to add regressors to your script:

--------------------------------------------------------
0. Modify your afni_proc.py command, to have it copy the
files to the 'results' directory via the -copy_files
option.

And in the resulting processing script...

1. Increment the -num_stimts parameter by the number of
additional regressors.

2. Add the extra stimuli after the motion parameters as
additional '-stim_file' options. A new line might
look something like:

-stim_file 27 respiration.1D -stim_label resp
--------------------------------------------------------

- rick