Hi Brian, 
I downloaded several DTI images from PROCESSED folder and checked them. They looks good (I attached screenshot from Slicer tool).
We don't use Diffusion Toolkit, but as I know from my experience with it - this tool supposed to reconstruct tensors from DWI images, so, you should provide preprocessed DWI images to have tensor image as output. Try to input to TrackVis DTI file directly, without Diffusion Toolkit step (because it's already tensors), if you will have problems with that, I suggest you to use files from AutoQC as input to Diffusion Toolkit. We have masks for structural data for the same subjects, you can register this masks to diffusion space. 

Best,
Roza

Roza Vlasova PhD., Postdoctoral Fellow
Neuro Image Research and Analysis Lab
Departments of Psychiatry
University of North Carolina at Chapel Hill