Hi Dharol,

This is different.

Your first method to get psc values looks fine.

The second method might be okay too, except that you would need
to either de-mean the regressors of no interest (like motion) or
include their means in the 3dcalc computation. That is probably
not worth the effort...

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When you scale the data, why should values outside the brain be
zero? Have you masked them? If not, their means should be 100.

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Note that afni_proc.py has been modified to no longer mask data
in orig space (by default, which one can override). I see you
are at least slightly in touch with that program, since you
limit the psc values to 200, so maybe the change was a surprise.
The program does output a comment about that when run.

We recommend not masking in orig space at all, but masking in
group space with an anatomical mask.

See the "MASKING NOTE" section of "afni_proc.py -help" for details.

- rick