I was able to run AFNI_proc.py with Qwarp where the skull was attached. However, again the registration wasn't the best but a little better than when skull-stripping is used.
It seems that the @toMNI_Qwarp did a better job with registration when I used that a while back. It seemed to omit the non-brain matter much better than Qwarp through AFNI_proc.py. Although there where other problems with @toMNI_Qwarp when I ran it (e.g., "droopiness"). I may try to run that again with the updated defaults and penality functinos.
Any ideas on why there would be a big difference between these two methods?
Thanks,
Danny
