Dear DTIPrep experts,
  I am trying to run brainmasking from the DTIPrep Pipeline modifying the defaults. It turns that braimaksing does not seem to strip skull. Using the "Slicer" flag it seems to run ok according to QCReport, but image QCed still has skull. Using any of the FSL options ends up with image math failure in the QCReport.
  Any solution? I've checked the protocol paths and everything seems to be where it should be . Usually I leave the "Brainmask_MaskedImage" field empty but I also have added a subject-specific mask in this field and it does the same.

Thanks in advance.