Re. figuring out env vars:
This is what I typically have on computers where I work (at the bottom of my ~/.afnirc), where I actually do literally have REF_TEMPLATES in all caps (but that is some personal choice you can obviously make!):
AFNI_GLOBAL_SESSION = /home/ptaylor/REF_TEMPLATES
AFNI_ATLAS_PATH = /home/ptaylor/REF_TEMPLATES
If on HPC, you might use something like /data/GROUP_DIR/USERNAME/REF_TEMPLATES, say.
If you are working exclusively with macaques, then you might want to have something like this, too, so that your "whereami" functionality would utilizing a macaque atlas:
AFNI_ATLAS_LIST = /home/ptaylor/REF_TEMPLATES/CHARM_in_NMT_v2.0_sym_05mm.nii.gz
And here is the full reference list, for details on these and more:
[
afni.nimh.nih.gov]
Re. alignment: that sounds different than the issue I had first assumed (exact same dsets with exact same code version/command on different systems giving different results). Indeed, mixing data across sessions can be tricky, because of coordinate and obliquity oddities/differences, esp. having those filtered through sphinx-to-normal re-positioning. But this is something we can discuss more in a separate thread.
--pt
