Issue linking python to AFNI:-(

AFNI Message Board
1

I installed AFNI but when I enter the command ‘afni_system_check.py -check_all’ , I get a message reading ‘env: python: No such file or directory’. So, I am able to launch AFNI but when I use the command ‘uber_subject.py’ I am not able to proceed with my analysis.

I have checked whether python is installed correctly by using the command ‘which python3’. I even tried to add python to my system’s path using the command
echo ‘export PATH=“/Library/Frameworks/Python.framework/Versions/3.11/bin:$PATH”’ >> ~/.zshrc_profile

I am using MacOS Ventura 13.2.1.

2

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:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/miniconda.html

–pt