Thanks for such a quick reply. I don't think there are any scalars with zero values, but I could easily be mistaken as all I am going off of is my reading of the probtrackx2 docs. If you would like I can send you the .vtk file.
Since my last post I was able to get this to work by running FIRST directly on the Freesurfer conformed T1. I am not sure where I went wrong, as my transformation from the input to the output worked fine outside of surf2surf.