Hello experts，
It seems there are some irregular overlaps in the initial QC overlap after applying obliquity correction following the completion of afni_proc.py(in the following picture），but other parts e.g.，the check vol alignment （EPI to anat）and MNI152_2009_template_SSW.nii to full_mask.nii seems normal.
This condition has never happened ever，I don’t if this results are acceptable? Or maybe I should do some other step?
Ciao-
The "Initial overlap" images in the "vorig" QC block, with the hot/cold overlay (EPI) on the black-and-white underlay (the anatomical volumes), just show the initial starting point of the EPI-anatomical overlap process. The second set of images---red lines (anatomical edges) over black and white underlay (EPI)---show the result of EPI-anatomical overlap. So, judge the alignment by the latter ones.
We show the initial overlap, because if the final EPI-anatomical alignment fails, poor initial overlap might be a reason for that. Here, the initial overlap doesn't strike me as too far off; and indeed, the alignment results seem good, which is the important thing.
The alignment video from the AFNI Academy here might be useful about this and other alignment considerations.
So, I don't see a problem here!
--pt
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