Dear Afni users,
I'm installing afni following this page: 1.1.8. macOS 12+ (Apple Silicon/ARM processor/chip: M1, M2, …) — AFNI, SUMA and FATCAT: v25.1.11
I have followed everything as written, but AFNI is not installed... It's my first time to install AFNI on my laptop. Could you help me?
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit Mach-O
cpu type: arm64
system: Darwin
release: 24.5.0
version: Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:25 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T6020
distribution: 15.5
number of CPUs: 12
user: soankim
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.1.11, anyos_text_atlas, May 23 2025, local
which python : /Users/soankim/miniconda3/bin/python
python version : 3.13.2
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 : 2
/Users/soankim/miniconda3/bin/python3.13
/opt/homebrew/Cellar/python@3.13/3.13.3_1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
python2 : 0
python3 : 4
/Users/soankim/miniconda3/bin/python3.13
/opt/homebrew/Cellar/python@3.13/3.13.3_1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/Library/Frameworks/Python.framework/Versions/3.11/bin/python3
/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
경고메시지(들):
패키지 ‘data.table’는 R 버전 4.3.3에서 작성되었습니다
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 -------------------------------
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
** failed to load module flask
-- flask is not required, but is desirable
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.11/bin/python3)
-------------------------------- env vars --------------------------------
PATH = /Users/soankim/miniconda3/bin:/Users/soankim/miniconda3/condabin:/Users/soankim/.pyenv/plugins/pyenv-virtualenv/shims:/Users/soankim/.pyenv/shims:/Users/soankim/.pyenv/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/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:/opt/homebrew/opt/python/libexec/bin:/Users/soankim/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin
PYTHONPATH =
R_LIBS = /Users/soankim/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
CC =
HOMEBREW_PREFIX = /opt/homebrew
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : missing
.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 : found AFNI_data6 under $HOME (948584M Avail)
top history: ...d GroupAna_cases/gen_datatables/ggc_dt_commands.tcsh
data dir : found AFNI_demos under $HOME
top history: 22 May 2025 [taylorp]: update subject QC directories
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 : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.5.3
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 17.0.0 (clang-1700.0.13.3)
brew gcc(s) : /opt/homebrew/bin/gcc-15
CommandLineTools SDK : MacOSX15.4.sdk
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* missing program: afni
* failure under initial "AFNI and related program tests"
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* python library matplotlib is required
(see AFNI install docs for details)
* please run: cp /Users/soankim/abin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* possibly missing atlases