Hi Christina,

You are probably right that there was a shift in your the tracts before. I am still not sure what the mrAnatXformCoords.m function is doing so I took it out. But more insidiously, I had assumed the original vox_to_ras transformation wanted the middle of my first voxel to be at (1,1,1), which is what I like to think of as voxel space (because you can just round the coordinates to get your voxel indices), however the middle of the first voxel should have been at (0,0,0) (per SPM conventions???). To emphasize why this confuses me to no end, DSI Studio and Track Vis put the middle of the first voxel at (0.5,0.5,0.5), so the bottom of the image volume is at (0,0,0)... any ways, I believe this is corrected!

I have attached another script which will perform the normalization from DKE output to MNI Image space (attached) and included an example data set which seems to work and I can't see an obvious shift. 

Sorry for the confusion!