Hello,
1. No. The input to 3dFWHMx should be residuals, such as a
residual time series, without any square root. You can see
examples of how it is used in afni_proc.py processing scripts,
such as
AFNI_data6/FT_analysis/s12.proc.FT.align .
2. That is very strange, unless your input is only 1 volume.
3. Yes. It should work well to average the 3dFWHMx parameters
across subjects for use at the group level.
Unfortunately, it is harder to tell how big the ACF parameters
are at a glance. So I cannot tell how reasonable yours look.
- rick