AFNI GUI fails to open following macOS 13 update


I’m trying to run AFNI using XQuartz 2.7.11 on my mac which I just updated to macOS 13.0. Before this iOS update, AFNI ran normally. Now when I call AFNI from my terminal, the GUI doesn’t open. Instead, I get the message below. Has anyone run into this and been able to fix it?

Thanks very much,

Precompiled binary macos_10.12_local: Oct 12 2022 (Version AFNI_22.3.02 'Lucius Verus')

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to ZS Saad for much encouragement

Initializing: X11++ AFNI is detached from terminal.


Could you post the output of the following command? -check_all

Here is the output:

(base) annamynick@Annas-MBP-10 ~ % -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 22.1.0
version: Darwin Kernel Version 22.1.0: Sun Oct 9 20:14:54 PDT 2022; root:xnu-8792.41.9~2/RELEASE_X86_64
distribution: 10.16
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/annamynick/abin/afni
afni version : Precompiled binary macos_10.12_local: Oct 12 2022
: AFNI_22.3.02 ‘Lucius Verus’
AFNI_version.txt : AFNI_22.3.02, macos_10.12_local, Oct 12 2022
which python : /Users/annamynick/opt/anaconda3/bin/python
python version : 3.7.4
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) – “Great Truth”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/annamynick/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/Users/annamynick/opt/anaconda3/bin/python3.7)
python2 : 0
python3 : 3

** have python3 but not python2

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

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

++ module loaded: matplotlib.pyplot
module file : /Users/annamynick/opt/anaconda3/lib/python3.7/site-packages/matplotlib/
matplotlib version : 3.1.1

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /Users/annamynick/opt/anaconda3/bin:/Users/annamynick/opt/anaconda3/condabin:/Users/annamynick/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/annamynick/Library/Python/2.7/bin:/usr/local/share/dotnet:/opt/X11/bin:~/.dotnet/tools:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/Users/annamynick/abin:/Users/annamynick/abin:/Users/annamynick/android-sdk-macosx/platform-tools/:/Users/annamynick/android-sdk-macosx/platform-tools/

DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (1908108M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/annamynick/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : /usr/local/Homebrew/Library/Homebrew/os/mac/version.rb:32:in `block in from_symbol’: unknown or unsupported macOS version: :dunno (MacOSVersionError)

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
** consider linking /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.66.2_1/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘zsh’…
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • just be aware: login shell ‘zsh’, but our code examples use ‘tcsh’

Try updating XQuartz to the latest version (now 2.8.2) and restart.

Thanks for that! I would suggest you update XQuartz to the newest version and restart your machine. That should fix it. But let me know!

Also looks like homebrew may need to either update or reinstall.

Just to follow up, updating X11 and brew and then restarting my computer fixed this issue.

Thanks very much!