I am also confused and I would like to have some clarification. Im not understanding correct if I should use or not the -fwhm flag in the 3dClustSim

In the webpage it says:
**** NOTICE ****
You should use the -acf method, NOT the -fwhm method, when determining cluster-size thresholds for FMRI data. The -acf method will give more accurate false positive rate (FPR) control.

-acf a b c = Alternative to Gaussian filtering: use the spherical
autocorrelation function parameters output by 3dFWHMx
to do non-Gaussian (long-tailed) filtering.
* Using '-acf' will make '-fwhm' pointless!
* The 'a' parameter must be between 0 and 1.
* The 'b' and 'c' parameters (scale radii) must be positive.
* The spatial autocorrelation function is given by
ACF(r) = a * exp(-r*r/(2*b*b)) + (1-a)*exp(-r/c)
>>---------->>*** Combined with 3dFWHMx, the '-acf' method is now a
recommended way to generate clustering statistics in AFNI![/color]

But the last part reffers to the combination with the 3dFWHMx