afni.nimh.nih.gov

Hi Vinny,
Difference is most likely because of resampling interpolation differences. adwarp uses linear, @auto_tlrc uses 5th order polynomial which would smooth the extreme values more than a linear interpolation would.
You can try using -rmode linear in @auto_tlrc and see if differences are less pronounced. These small blurring differences should not affect the results much.
z