Detritus Wiki

You can use:

$ fslmaths original.nii -kernel gauss 2.1233226 -fmean smoothed.nii

The gaussian kernel takes its argument as sigma in mm instead of the FWHM, but you can see how to convert between these two values here: http://mathworld.wolfram.com/GaussianFunction.html

Basically, divide your FWHM (in mm) by 2.3548 to get sigma.