Hi,
  After troubleshooting some issues with the paths of the tools, it turns that brainmask does not work because he cannot find subj_IDWI.nrrd. I noticed that when I check "compute the DTI" (usually I uncheck this last step), a subj_IDWI.nrrd file is generated. Does it make sense?

 Also, when trying to do visual inspection, it only saves the changes to a subj_QCed_VC.nrrd file if the DTI tensor had previously been computed. Does that make sense also or it is just something related to my computer?

Thanks