Hi Tyler,
If you are going to apply RETROICOR on a per-slice basis, then that
will have to happen before 3dTshift.
The warning in 3dTshift should apply to use of Fourier interpolation,
which is not necessary to use. Note that afni_proc.py applies quintic
interpolation by default, via "3dTshift -quintic".
When RETROICOR is applied using afni_proc.py, it is slice based. The
default processing order (in that case) is despike, ricor, tshift,
volreg, etc. The ricor block is done with the regressors from Ziad's
RetroTS program, which implements the Glover and Birn methods.
- rick