Also, as of last night's update, you can use the following 2 new options to adjust the -stim_times* times:

-stim_times_millisec
This option scales all the times in any '-stim_times_*' option by
0.001; the purpose is to allow you to input the times in ms instead
of in s. This factor will be applied to ALL '-stim_times' inputs,
before or after this option on the command line. This factor will
be applied before -stim_times_subtract, so the subtraction value
(if present) must be given in seconds, NOT milliseconds!

-stim_times_subtract SS
This option means to subtract 'SS' seconds from each time encountered
in any '-stim_times*' option. The purpose of this option is to make
it simple to adjust timing files for the removal of images from the
start of each imaging run. Note that this option will be useful
only if both of the following are true:
(a) each imaging run has exactly the same number of images removed
(b) the times in the 'tname' files were not already adjusted for
these image removal (i.e., the times refer to the image runs
as acquired, not as input to 3dDeconvolve).
In other words, use this option with understanding and care!
** Note that the subtraction of 'SS' applies to ALL '-stim_times'
inputs, before or after this option on the command line!
** And it applies to global times and local times alike!
** Any time (thus subtracted) below 0 will be ignored, as falling
before the start of the imaging run.
** This option, and the previous one, are simply for convenience, to
help you in setting up your '-stim_times*' timing files from
whatever source you get them.