Can you be a little more specific about what processing you have done with FMRI-prep, and what you would like to do with AFNI?
And what kind of data do you have---resting state, naturalistic or task-based?
I believe FMRI-prep covers a subset of what would typically be done with afni_proc.py, for example not including what would be contained in the "regress" block. Typically as afni_proc.py runs, it generates items for use in the regress block, so I guess you would want to specify what equivalents there are, again depending on what you want to calculate.
--pt
