Hi,

this is the output of afni_system_check.py -check_all:

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              21.4.0
version:              Darwin Kernel Version 21.4.0: Fri Mar 18 00:46:32 PDT 2022; root:xnu-8020.101.4~15/RELEASE_ARM64_T6000
distribution:         12.3.1
number of CPUs:       10
apparent login shell: zsh
shell RC file:        .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /applications/AFNI/abin/afni
afni version         : Precompiled binary macos_10.12_local: Mar 20 2022 
                     : AFNI_22.0.21 'Hadrian'
AFNI_version.txt     : AFNI_22.0.21, macos_10.12_local, Mar 20 2022
which python         : /opt/homebrew/bin/python
python version       : 2.7.18
which R              : /Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R
R version            : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/applications/AFNI/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
    python  : 1   (/opt/homebrew/Cellar/python@2/2.7.18/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    python2 : 1   (/opt/homebrew/Cellar/python@2/2.7.18/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    python3 : 3 
      /Library/Frameworks/Python.framework/Versions/3.10/bin/python3.10
      /opt/homebrew/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/bin/python3.9
      /usr/bin/python3


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        
        oo Warning: 
           These packages are not installed on the computer: afex!
        

R RHOME : /Library/Frameworks/R.framework/Resources

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required

-- python binaries under /usr/local/bin:
    /usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.10/bin/python3.10)

-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/3.10/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/applications/AFNI/abin:/Library/Frameworks/R.framework/Versions/3.6/Resources/bin

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /applications/AFNI/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.1

which brew           : /opt/homebrew/bin/brew
brew version         : Homebrew 3.4.4

-- for PyQt4 under brew, consider running:
   brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
   -- found 'libXt' dylib files:
      /opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
   (so afni and suma may fail)

=========================  summary, please fix:  =========================
*  just be aware: login shell 'zsh', but our code examples use 'tcsh'
*  missing R packages (see rPkgsInstall)
*  python library matplotlib is required
   (see AFNI install docs for details)
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)
*  OS X version might be old
*  consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace

I see that AFNI also does not find matplotlib, but matplotlib is installed. Furthermore AFNI relies on Python2, but not Python 3. I assume thats due to the wrong PATH settings and so on... How can I fix this? I tried using

ln -s /usr/local/bin/python3 /usr/local/bin/python

as suggested again by Rick, but get access denied. I think that we faced this problem some months ago when you helped me, Paul.

And this is the output of

tcsh
python -V
/usr/bin/env python -V
which python

Python 2.7.18
/usr/bin/env python -V
which python[MacBook-Pro-16:~] philipp% /usr/bin/env python -V
Python 2.7.18

I think my AFNI installation or "linking" with Python is really messed up. Please let me know what changes I should do. For example, what PATH line should I add to my .zshrc file (which is invisible in the home folder, and can be seen by pressing CMD + shift + . )? It would be cool if I can at least fix the matplotlib problem, since otherwise I won't get QC images after preprocessing and so on.

To make things more clear, here is the content of my .zshrc file.

# Prompt design
PROMPT='%B%F{201}%n%f%b %1~ '

# auto-inserted by @update.afni.binaries :
export PATH=$PATH:/applications/AFNI/abin
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace

# Linking R and Python
export PATH=$PATH:/Library/Frameworks/R.framework/Versions/3.6/Resources/bin
alias python=/usr/local/bin/python3

# The following lines were added by compinstall
zstyle ':completion:*' completer _complete _ignored _approximate
zstyle ':completion:*' list-colors ''
zstyle :compinstall filename '/Users/philipp/.zshrc'

autoload -Uz compinit
compinit
# End of lines added by compinstallexport PATH="/opt/homebrew/opt/python@3.10/bin:$PATH"

Edited 1 time(s). Last edit at 04/04/2022 01:16PM by Philipp.