Hi Daniel,
Just for clarification, first I would use @auto_tlrc and auto_warp py to do an initial affine registration and then non-linear registration of my DTI data to standard space. Then I would use these matrices for 3dNwarp to go back to diffusion space.
*At what point do I put in my ROI to warp to diffusion space? Does this occur at 3dNWarp apply?
@auto_tlrc -base TT_N27+tlrc -input strip_shift+orig. -no_ss \
-init_xform AUTO_CENTER
# nonlinearly align to template
auto_warp.py -skip_affine -base TT_N27+tlrc -input strip_shift+tlrc
Thanks,
Emily
