Hi Bridget,
You should be using Usage 1 (see
help) for transforming your structural data to standard space and then Usage 2 to apply the same transform (created in in Usage 1) to your functional data. So a standard pipeline might look like this:
#transform anatomical, assumes anatomical has skull on, otherwise add -no_ss
@auto_tlrc -base TT_N27+tlrc -input Subj_Anatomical+orig -init_xform AUTO_CENTER
#transform functional EPI
@auto_tlrc -apar Subj_ Anatomical+tlrc -input Subj_EPI+orig -dxyz 3
Is this what you're currently using?