Hi, Asya-

In your output "results" directory from afni_proc.py, there should be a "QC_${subj}" directory, which contains the afni_proc.py quality control (APQC) HTML.

Can you go into that results directory, and type:

afni_open -b QC_*/index.html

.... to open the APQC HTML in your default web browser (or you can open that file in any browser you want).

Can you check the EPI-to-anatomical alignment in the "ve2a" block, and the anatomical-to-template alignment in "va2t"? Please let us know if whether each of those resulting alignment steps looks good or poor? I am guessing if "-tlrc_opts_at -init_xform AUTO_CENTER" was required that the va2t alignment might have failed. Is the anatomical oblique? (What is the output of "3dinfo -obliquity DSET_ANAT"?)

If the EPI-to-anatomical alignment does not look good, could you please check out the image of initial EPI-anatomical overlap image that shoudl be in the top "vorig" block---is there good overlap between the initial EPI-anatomical?

thanks,
pt



Edited 1 time(s). Last edit at 10/18/2022 09:27AM by rick reynolds.