afni.nimh.nih.gov

> 1) Should I loop through this sub-brik with 3dFWHMx, where the loop index is used to give 3dFWHMx one sub-brick at a time or can I just give it the full 4D-volume?

Do it on the 4D data (residuals for the model).

> 2) Should I use any of these option?

Those options do not seem to be applicable in this case.

> 3) Should I for structural data still use -ACF or is classical -fwhm sufficient?

ACF is preferable.

Gang