Hello,
I have been trying to install afni following the quick setup instructions for Mac OS 12+ apple silicon. My computer has an M3 chip. I installed python 3.12.4, and followed the quick setup steps to the letter. It seems like it all goes wrong with step E:
tcsh OS_notes.macos_12_ARM_b_user.tcsh
which gives the following output:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 35201 0 --:--:-- --:--:-- --:--:-- 35565
set os = `uname -s`
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = `uname -m`
uname -m
if ( 0 ) then
set rver = `R --version | head -n 1 | cut -d ' ' -f 3`
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : arm64
CPU : arm64
echo R ver : 4.3.1
R ver : 4.3.1
echo
defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 412k 0 --:--:-- --:--:-- --:--:-- 414k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/wp/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- no current AFNI package found in path...
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f
-- attempting to install package anyos_text_atlas under
install dir: /Users/wp/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 594 0 --:--:-- --:--:-- --:--:-- 600
++ no update needed
/Users/wp/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/wp/abin
env: python: No such file or directory
Like I mentioned I do have python 3.12.4 installed. I tried substituting running the last command by putting python3 in front of it:
python3 /Users/wp/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/wp/abin
Which seemed to do something other than crashing. Still the final check up didn't do anything as it couldn't find the file:
afni_system_check.py -check_all
-bash: afni_system_check.py: command not found
I tried removing the abin directory as well as any other files related to the installation and tried again with a conda environment. Still the same problem.
I am not sure what am I doing wrong. My suspicion is that the multiple attempts at installing are somehow interfering with trying to install again. I believe I have removed everything from previous attempts but I may be wrong.
Any guidance and help is greatly appreciated.