Hi Im also having the problem to open AFNI from terminal,
lbohorquez@PSYC-CRI-10822:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.2.0
version: Darwin Kernel Version 19.2.0: Sat Nov 9 03:47:04 PST 2019; root:xnu-6153.61.1~20/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (does not exist)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/lbohorquez/abin/afni
afni version : Precompiled binary macos_10.12_local: May 4 2020
: AFNI_20.1.06 'Otho'
AFNI_version.txt : AFNI_20.1.06, macos_10.12_local, May 04 2020
which python : /usr/bin/python
python version : 2.7.16
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/lbohorquez/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/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 : 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 : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/lbohorquez/abin
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 /Users/lbohorquez/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.2.15
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /usr/bin/python
++ 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: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: MISSING non-login setup file .bashrc
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* insufficient data for AFNI bootcamp
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
