I guess i have a follow up question.
with 3dvolreg, we get to specify the -tshift ii. the manual says this is like running 3dTshift first then a 3dvolreg. my question is, how do we specify which slice to be the reference slice (time 0) ? it doesn't look ii is the parameter (The integer 'ii' is the number of time points at the
beginning to ignore in the time shifting. link: [afni.nimh.nih.gov])

Thanks again.