Hi Emily,

If you do not censor and you do not bandpass in afni_proc.py, then passing
the errts dataset would be fine. In that case you would not need any -ort
option (since those terms would have already been removed).


Alternatively, you could still censor in afni_proc.py, depending on what
you want to do. In addition to X.xmat.1D (with censoring), the AP script
would produce X.nocensor.xmat.1D, which is the same matrix, but before any
censoring (i.e. as if 3dD had no -censor option).

But run AP.py without bandpassing (you could leave that in, but would then
have to figure out how to remove it from the X-matrix, which we could help
with, it would not be difficult).

Then the input to 3dRFSC would be the same input to 3dDeconvolve (I will
assume you only have 1 run here), plus the '-ort X.nocensor.xmat.1D' option,
along with -nodetrend.

Or you can go with what you have, and just remove the -ort option.


Regarding the physio regressors, if they are created via RetroTS, then they
could be removed via afni_proc.py (very early, even before 3dTshift, since
they are sliced-based regressors). See AP example 5c, but maybe without the
bandpass option. That is up to you.

- rick