Hi Wolfram,
How much blur is in the original data depends on the scanner
and protocol. But it is generally more than zero, which means
the applied blur will be less than the resulting (estimated)
blur.
When running 3dFWHMx, be sure to apply a mask, and process
just one run at a time. You might consider what afni_proc.py
does with it, when you ask to estimate the blur.
Note also that afni_proc.py can do censoring, bandpassing and
regression all in one step (so censoring is proper). So it
might be good to try it out, at least to compare with your own
processing steps.
If this is resting state data, consider example #9 from the
help output.
- rick