Dear Afni experts,

I am a new user of Afni and I am using it for analyzing rs-fMRI data.

I was getting warning messages about obliquity of data, and alignment between anat and EPI was miserable. I have tried a few things and they have worked, but I am not sure which one is the best option and why?

This is what I have tried:

1- I used 3dwarp on anat alone and then on anat and EPI both before running the afni_subject.py, and it improved the alignment in both cases.

2- I used 3drefit on n anat and EPI both, and alignment was no better than that in 1.

3- I used giant_move only and alignment is quite the same as in 1.

Now, I am confused. I am not sure where the actual problem is. Is it that the subject moved between the two scans (which is dealt with by giant-move), or that there is real obliquity (fixed by 3dwarp) or that there is bad metadata (fixed by 3drefit)? Please help.

Thanks