Dear Hamed,
In case your functional volumes were smoothed I would smooth the GM files accordingly before applying a threshold to generate the mask (or alternatively, mask the functional volumes and only then apply smoothing). The decision should be based on where GM is present in the processed images, not where GM was present initially.
I wouldn't go with any such masks though (at least as long as you don't have acquired functional data with very high resolution). The unmasked maps provide some useful information. "Activations" in ventricles and/or WM might point to some problems with drift or head motion. Once you apply a mask only the boundary areas of the artefact might remain and look like "nice" activations in basal ganglia.
Best regards
Helmut
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