Hi Andrew,
That motion is tiny, but looks fine (i.e. a great subject! :). It
looks like 7 valid runs of maybe 144 TRs per run (based on motion
between runs).
In your case, 720 is a multiple of the reps (TRs per run) and is
therefore from motion between runs. There is no need to censor such
motion. However yes, you could feed 720 in via -CENSORTR. While
720 is a 'global' TR, your -stim_times do not need to be global,
that would be a separate consideration.
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It looks like 1dFlagMotion should be executed once per run.
Note that 1d_tool.py has a -derivative option, as well as -set_nruns.
So you could use something like example 7 (1d_tool.py -help) to help
look for large motion.
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We do not generally use 3dFourier (as you can tell since afni_proc.py
does not even include the ability). The polynomial baseline in
3dDeconvolve serves as a low-pass filter, while tracking degrees of
freedom.
- rick
