From the help for afni_proc.py:
TIMING FILE NOTE: ~2~
One issue that the user must be sure of is the timing of the stimulus
files (whether -regress_stim_files or -regress_stim_times is used).
The 'tcat' step will remove the number of pre-steady-state TRs that the
user specifies (defaulting to 0). The stimulus files, provided by the
user, must match datasets that have had such TRs removed (i.e. the stim
files should start _after_ steady state has been reached).
https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html
In other words, you have to adjust the timing files yourself.
