Hi, Xin-

There should be an output QC HTML in your afni_proc.py results directory; it will be the "simpler" one, and in the future you might want to add "-html_review_style pythonic" to your afni_proc.py command.

But anyways, based on your subject ID, there should be a directory called "QC_s0" in the results directory; can you open the "index.html" file there, either by navigating to it and clicking on it, or perhaps just using a browser from the command line? For example, on Linux with Firefox install, you could type:

firefox QC_s0/index.html

from the results directory.

More details about this are provided here:
[afni.nimh.nih.gov]
... but in the top 2 sections are the ve2a (volumetric EPI to anatomical) and va2t (volumetric anatomical to template) QC blocks. If you could post those images here, we could assess each of those individual alignment steps?

If you would like to re-run the QC with the nicer Pythonic form (for motion and other plots), assuming you have Python and its matplotlib module installed, you could do the following:

# get a script to redo the QC part that happens at the end of afni_proc.py, 
# which will run it in Pythonic form
wget [raw.githubusercontent.com]

# execute the script: with no arguments, it runs in the current directory;  or, you can put 
# a list of one or more results directories from afni_proc.py output,
# and it will run in each.
tcsh redo_apqc.tcsh

This will move any existing APQC (afni_proc.py QC directory) to a backup old_QC_*, and then create a new QC_${subj} again in the same spot, where ${subj} is the subject ID.

--pt