Hi Rick,

After looking into our afni_proc.py script a bit more, we decided that which file we use depends upon which way we decide to run the Qwarp scripts and what we think will be better. If we keep the "-volreg_align_e2a" command, then using the anat_final+orig anatomy would be ideal since that may produce the best fit between the anatomy and stats-epi file when we Qwarp it later. Since the epi output is aligned with the anat_final, when we go apply the MNI-Qwarp-anat matrix to the epi, it will already be somewhat aligned with the original anat maybe allowing a smoother/better transformation.

If we omit the -volreg_align_e2a, we would most likely use the skull-stripped anatomy "spgr_strip+orig" since that is the least processed of the anatomys after skull-stripping. Then all normalization would be done after pre-processing.

We are planning on going with the first method and checking how well it works.

Thanks,

Danny