Hi Shana-
The correct (read: most common, easiest, more tested) approach is:
1) Freesurfer on your original T1 anatomicals (with the skull on)
2) run @SUMA_Make_Spec_FS on the output folder
3) Use afni_proc.py (or uber_subject.py). See example 8. This will automatically perform the alignment between Freesurfer's anatomical, the surfaces, and the EPI. If you feed it the std.141 files, then your outputs will already be on a common mesh. Note that example 8 (and all surface based analysis pipelines) do not have a TLRC block. This is because surface alignment is performed differently (via MapIcosahedron).
If you don't want to use afni_proc.py (you really should), then take the TLRC block out of your processing and then use @ SUMA_AlignToExperiment to the subject space (+orig) file.
And definitely do not send your TLRC files through Freesurfer.
-Peter
