Hello, I am having issues installing AFNI on my Apple M2 Max with macOS 14.7.2 using a bash shell. I have gone through all of the instructions to the best of my ability and created a conda environment for the python functions. One issue is that I'm having trouble automatically adding abin to my path upon startup. This is my .bashrc file:
eval "$(/opt/homebrew/bin/brew shellenv bash)"
export PATH=${PATH}:/opt/homebrew/opt/python/libexec/bin
-------------------------------------------------------
for AFNI: auto-inserted by init_user_dotfiles.py
add AFNI abin to PATH
export PATH=${PATH}:/Users/jourdan.pouliot/abin
set up tab completion for AFNI programs
if [ -f $HOME/.afni/help/all_progs.COMP.bash ]
then
source $HOME/.afni/help/all_progs.COMP.bash
fi
-------------------------------------------------------
-------------------------------------------------------
for AFNI: auto-inserted by init_user_dotfiles.py
look for shared libraries under flat_namespace
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace
-------------------------------------------------------
But even when I add abin to my path during the session. I am unable to start AFNI using the afni command. Below is the output for afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Fri Nov 15 15:11:49 PST 2024; root:xnu-10063.141.1.702.7~1/RELEASE_ARM64_T6020
distribution: 14.7.2
number of CPUs: 12
user: jourdan.pouliot
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.0.07, anyos_text_atlas, Feb 25 2025, local
which python : /Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/bin/python
python version : 3.12.9
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)
instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 1 (/Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/bin/python3.12)
python2 : 0
python3 : 2
/Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/bin/python3.12
/usr/bin/python3
testing ability to start various programs...
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
build_afni.py : success
uber_subject.py : success
3dMVM : FAILURE
Error in library(data.table) : there is no package called ‘data.table’
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
rPkgsInstall : FAILURE
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
tcsh version : 6.21.00
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/lib/python3.12/site-packages/matplotlib/pyplot.py
matplotlib version : 3.10.0
++ module loaded: flask
module file : /Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/lib/python3.12/site-packages/flask/init.py
flask version : 3.1.0
++ module loaded: flask_cors
module file : /Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/lib/python3.12/site-packages/flask_cors/init.py
flask_cors version : 3.0.10
-------------------------------- env vars --------------------------------
PATH = /Users/jourdan.pouliot/miniconda3/envs/py3_afni_mid/bin:/Users/jourdan.pouliot/miniconda3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Users/jourdan.pouliot/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 2
CONDA_DEFAULT_ENV = py3_afni_mid
CC =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- good: .cshrc seems to contain 'source .tcshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
no modifications needed across 3 dot files
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
** no package manager found (okay for bootcamp)
which git : /usr/bin/git
git version : git version 2.39.5 (Apple Git-154)
which gcc : /usr/bin/gcc
gcc version : Apple clang version 16.0.0 (clang-1600.0.26.6)
brew gcc(s) : /opt/homebrew/bin/gcc-14
CommandLineTools SDK : MacOSX15.2.sdk
========================= summary, please fix: =========================
- just be aware: login shell 'bash', but our code examples use 'tcsh'
- shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
- missing program: afni
- failure under initial "AFNI and related program tests"
- AFNI programs show FAILURE
- missing R packages (see rPkgsInstall)
- please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages) - possibly missing atlases
I would appreciate any help you can give me.
Best wishes,
Jourdan