You should be able to remove the 'tlrc' block,
and -tlrc options (you have -tlrc_base). Then
remove the "+orig" from your -copy_anat dataset,
i.e. use: -copy_anat $subject-$phase-t1mprage .
On a separate topic, are you sure about using
-regress_censor_motion 3.0? That is a per-TR
motion limit, making it pretty high. The outlier
censoring should mitigate that, though.