Hi Pat,
The problem, I suspect, is that your functional data are not aligned with your anatomical data in +orig space. If that is the case, then applying the transform from the anatomical data to the EPI data will not get the latter to tlrc space.
If your anatomical in +orig space is not aligned with your EPI, then one solution would be to transform the T1 anatomicals to a T1 template (like you did in the first command), then transform the EPI to an EPI template (like TT_EPI+tlrc). The -apar option only works when datasets are aligned in +orig space in the beginning.
cheers,
-ziad