[Freesurfer] a white matter mask that excludes sub-cortical structures

Hello,

I am trying to create a white matter mask that excludes sub-cortical structures for use in calculating FA from a dti scan. I am still using version 3.0.5 for now. I was considering combining the surface white matter mask and the aseg mask of the sub-cortical structures, but was not sure if this was valid. I am concerned because the surfaces are calculated separetly from the aseg and there will likely be some areas of disagreement between the two, for example in the hippocampus. Any suggestions would be appreciated. Does the new version 4.0.0 dti package include any helpful tools?

Chris Bell University of Minnesota