Hi, Osman-
To check the alignment specifically before looking at stats, I looked at the ve2a QC images in the APQC HTML you sent. It looks quite good now (see attached).
It looks like you are performing a resting state analysis, because you don't have any stimulus files/GLTs in your afni_proc.py command. There is some QC for that in the APQC HTML as well---the seedbased correlation (DMN seed) image is attached---it looks OK; the correlation might be a bit low in some places, but with the transparent thresholding we see "orange" in places we would expect.
I thiiiink your shared image here is of the actual time series values of one EPI, just one of the EPI volumes. Am I understanding this correctly? Because I don't think it is really "correlation" being shown, which you commented about in your question. With scaling on, I think one might expect the noise outside the brain to have large values like that above some kind of threshold. I don't think that is really a worry or sign of badness. Using something like seedbased correlation would be a better test of data quality.
--pt
