Hi, Kara-

You can apply the same shift that got applied to your anatomical (when aligning its center of mass to the template with @Align_Centers) to the EPI, by treating the EPI as a "child" dataset. You would want to copy each of the "-dset .." and "-child .." inputs before running @Align_Centers in this case, because the program will now overwrite each (that is, internally adjust the origin information in the file's header).

Using your file names, this could be done before running @SSwarper in general with (*please read note below before running on your current subj*):

3dcopy $scan_dir/$subj.anat.uni+orig $subj.anat.uni.ac
3dcopy EPI EPI_NEW

@Align_Centers \
-cm \
-no_cp \
-dset $subj.anat.uni.ac+orig \
-base TT_N27_SSW.nii.gz
-child EPI_NEW+orig

... and then use EPI_NEW+orig as your afni_proc.py inputs with "-dsets ...".

Note that, in your case here, you have already run @SSwarper; so, in order to not have to run it again, I would do the following:

3dcopy $scan_dir/$subj.anat.uni+orig TEMP_ANAT
3dcopy EPI EPI_NEW

@Align_Centers \
-cm \
-no_cp \
-dset TEMP_ANAT+orig \
-base TT_N27_SSW.nii.gz
-child EPI_NEW+orig

.... now, you can ignore TEMP_ANAT-- it just ends up in the exact same pre-aligned-to-template state that your input to @SSwarper did (but it doesn't overwrite it). Now, you should be able to input EPI_NEW+orig into your afni_proc.py command.

A question though: why does your current input EPI to afni_proc.py command start with pb.00* ? That makes it look like it has already been through some kind of processing with afni_proc.py, which I don't understand.

--pt