Hi-
I believe the issue is that the Python programs are referred to with "python", not "python3". Could you please try copy+pasting the following in a terminal:
ln -s /usr/local/bin/python3 /usr/local/bin/python
so that the command "python" will link (or essentially point) to what is called "python3".
If you then open a new terminal, does "afni_system_check.py -check_all" now execute OK?
For getting/managing Python modules (numpy and matplotlib, primarily) on a Mac, miniconda is often useful, as well, as described in these AFNI notes:
[
afni.nimh.nih.gov]
--pt