Hi Lucy,
You are right about to3d. It does not touch the data at all
(unless you do byte swapping). But during the conversion to
acpc and then tlrc views, the data will be resampled.
If you do not like the default resampling done in afni, you
can go back and use adwarp with the -resam option, to specify
a different resampling method.
But overall, the values do not really get scaled, if that is
your concern. If you really want them to retain the original
values, consider using the nearest neighbor resampling method
(-resam NN).
- rick