Dear Doug,

I figured out the mistake I was making, which was that I ran:

freeview -v orig.mgz wmparc2diff.mgz:colormap=lut lowb.nii.gz:reg=register.dat -f lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal &

Here the lowb, orig, and white surfaces were consistent. Since wmparc2diff.mgz is in diffusion space, it was bound to be mismatched with the lowb & white surface lines. When replacing wmparc2diff.mgz with wmparc.mgz, it is no surprise that there is a much better match between the white matter parcellation & lowb.

There is a very good match between lowb and wmparc2diff, when running, per the documentaiton,

freeview -v lowb.nii.gz wmparc2diff.mgz:colormap=lut -f lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal &

However, the lh.white and rh.white surfaces do not change. I suppose this is because those surfaces are not for volumes registered to the diffusion space. Does that make sense? Or would the lh.white and rh.white automatically adjust to diffusion space?

Thank you.

Best, Chintan