Great suggestions. Thanks very much for your advice!
In answer to your questions/suggestions, smoothest does seem to be applying a mask. While it will not run without inputting a mask, switching the mask changes the smoothness values.
Second, neither 3dFWHMx nor smoothest seem to simply be averaging the smoothness values calculated across the individual volumes.
Running 3dFWHMx on each volume separately (from fslsplit) and averaging across volumes for the x, y, and z dimensions yields:
x = 9.886185862
y = 9.917113793
z = 9.207430345
while doing the same thing using smoothest yields
x = 11.15205172
y = 11.22923862
z = 10.41682207
Best,
Jessica
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