Hi AFNI experts,
I was wondering if there is a "best" point during preprocessing to do the registration to a standard template? I know some programs do it before subject-level statistics, while others do it after.
I am currently running everything within AFNI_proc.py. I am wondering if I can do all the preprocessing (e.g., motion & slice-time correction, blurring, convert to mean % signal change, etc.) using proc.py, then do registration in a separate script (Qwarp or FSL's FNIRT). Then run 3dDeconvolve after registration. Will this be appropriate?
The reason I plan to do the registration outside of proc.py is that for our dataset, Qwarp is not doing a great job in proc.py. I either plan to see if the @toMNI_Qwarp option (or FNIRT) will work better for registration and then apply it to the EPI data.
Thanks,
Danny
