Thank you for accepting me into the community. I came across an oddity that I wanted to clear up. By default the tshift option in afni_proc.py will put the reference volume at t=0 while 3dTshift itself has the default reference volume at TR/2. Most commonly and mathematically plausible would be the TR/2 option, so I was wondering what the reasoning is, in putting it to the first volume?
Thanks for the help.