Howdy-
I think we will need some more details to be able to diagnose+prescribe here...
Could you please let us know:
+ alignment command you ran---I am not even sure if we are talking about anatomical-template alignment, EPI-anatomical, or the combination thereof; and if nonlinear alignment between the anatomical and template are involved, what program is being used (3dQwarp, auto_warp.py or the recommended @SSwarper)?
+ what is the "issue" with this dataset? Can you please attach an image.
+ also, what version of AFNI are you using ("afni -ver")
thanks,
pt