The afni_proc.py documentation suggests that one can specify cardiac/respiration data to be regressed out of the fmri signal using (at minimum) the following flags:

-do_block despike ricor
-ricor_regs slibase*.1D
-ricor_regress_method across-runs
-ricor_regs_nfirst 3

However, in the documentation (e.g. example 5a) the '-ricor_regress_method' is not added.

afni_proc.py -subj_id sb23.e5a.ricor \
-dsets sb23/epi_r??+orig.HEAD \
-do_block despike ricor \
-tcat_remove_first_trs 3 \
-ricor_regs_nfirst 3 \
-ricor_regs sb23/RICOR/r*.slibase.1D \
-regress_motion_per_run

It appears that the signal is regressed during pre-processing. If this is the case, what is the difference in the final data when the card/resp regressors are also included in the final regression (e.g. using '-ricor_regress_method')? Is there a standard process for resting-state data? The documentation also list an option '-regress_apply_ricor yes' to include the regressors in the final model. Is this any better/worse/different than using '-ricor_regress_method'.