The Slicer brain masking is not the best (which is likely why there's still skull in the image,I assume that something was removed?). For the FSL option, our tool ImageMath is used. Unfortunately there are other tools that have also an ImageMath binary (e.g. ANTs or Rview), so you need to make sure that the path to DTIPrep's ImageMath folder has to be before the paths of the other tools.

I usually use bet with IDWI

Martin