Hi Bridget,
I would recommend using
align_epi_anat.py to do the EPI to anat and EPI to standard space transform. You can use syntax similar to the example:
@auto_tlrc -base ~/abin/TT_N27+tlrc -input sb23_mpra+orig
align_epi_anat.py -anat sb23_mpra+orig -epi epi_r03+orig \
-epi_base 6 -child_epi epi_r??+orig.HEAD \
-epi2anat -suffix _al -tlrc_apar sb23_mpra_at+tlrc
Better still, would be to use
afni_proc.py for processing your data, which will take care of all of the preprocessing and single-subject analyses.