Hi Paul,

Quote
When you say that you get "bad results", what does that mean---if you put your recentered data into afni_proc.py, is the EPI-anatomical alignment not good (ve2a block), or is the anatomical-template alignment not good (va2t block)?

By "bad results" I refered to the new or lower image attached, that is, the result of 3drefit (and not a preprocessed result by AFNI proc).

I remember that when I previously ran AFNI proc on such "bad" anatomical-functional overlaps, I often got bad or simply messed up alignment results from AFNI proc. Then, I ran the same 3drefit script as shown above (you helped me here long ago, suggesting to run this script), which resulted into a really nice anatomical-functional overlap.

However, this time the functional scan still looks so oblique after running 3drefit. In fact, even after running 3drefit the oblique degree looks almost like before, as if I only ran

 -oblique_recenter

but not

-deoblique

Thats why I aimed to a get good overlap before running AFNI proc at all (I did not even run AFNI proc yet).
So thanks for your answer, I did really not expect that *this* overlap result by 3drefit can be good enough for proper preprocessing (which I will try out after SSwarper is ready and then probably report back here in case I face further problems that I cannot solve on my own).

One more question:
Some subjects’ raw anatomical and functional scans are in +orig space, while others are in +tlrc space. I considered that in the 3drefit script by simply changing the code lines to +orig or +tlrc, depending on the subject. Next, I would feed the results of 3drefit to SSwarper and subsequently to AFNI proc. Does AFNI proc handle both the +orig and +tlrc files fine, or do I have to apply @auto_tlrc on the +orig subjects even before running SSwarper and AFNI proc?