afni.nimh.nih.gov

I would first look at the inputs to 3dFWHMx carefully. The program works by computing statistics of the spatial first differences of the input, and that is only possible if there are a lot of neighboring voxels in the mask. In the worst case, if your mask comprised only the 'white' squares on a chessboard, then 3dFWHMx would fail as you describe.