Hi everyone,
I recently installed AFNI in a new m4 Mac.
I'm preprocessing some data now, using a pipeline that I used in the past. I'm trying to use @auto_tlrc, but I get error messages like the one reported below.
I'd appreciate some help understanding what I'm doing wrong : )
Thanks,
Nicola
@auto_tlrc -no_ss -base /Volumes/HardDisk/CNP/CNP_REST/MNI152_T1_2009c+tlrc -input sub-10171.struc_al+orig
usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...
conda: error: argument COMMAND: invalid choice: '/Volumes/HardDisk/CNP/CNP_REST/MNI152_T1_2009c+tlrc' (choose from activate, clean, commands, compare, config, content-trust, create, deactivate, doctor, env, export, info, init, install, list, notices, package, remove, rename, repoquery, run, search, tos, uninstall, update, upgrade)
This is the output of my system_check:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm64
system: Darwin
release: 24.3.0
version: Darwin Kernel Version 24.3.0: Thu Jan 2 20:22:58 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T8132
distribution: 15.3.1
number of CPUs: 10
user: nicolasambuco
apparent login shell: sh
shell RC file: .profile (does not exist)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/nicolasambuco/abin/afni
afni version : Precompiled binary macos_13_ARM: Jun 4 2025
: AFNI_25.1.11 'Maximinus'
AFNI_version.txt : AFNI_25.1.11, macos_13_ARM, Jun 04 2025, build
which python : /Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/bin/python
python version : 3.9.21
which R : /usr/local/bin/R
R version : R version 4.5.0 (aarch64-apple-darwin20)
instances of various programs found in PATH:
afni : 1 (/Users/nicolasambuco/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/bin/R)
python : 2
/Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/bin/python3.9
/opt/homebrew/Cellar/python@3.13/3.13.3_1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
python2 : 0
python3 : 3
/Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/bin/python3.9
/opt/homebrew/Cellar/python@3.13/3.13.3_1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/usr/bin/python3
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
build_afni.py : success
uber_subject.py : success
3dMVM : success
rPkgsInstall : success
------------------------ 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 : success
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.9.2
++ module loaded: flask
module file : /Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/lib/python3.9/site-packages/flask/__init__.py
flask version : 3.1.0
++ module loaded: flask_cors
module file : /Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/lib/python3.9/site-packages/flask_cors/__init__.py
flask_cors version : 3.0.10
-------------------------------- env vars --------------------------------
PATH = /Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/nicolasambuco/miniconda3/envs/py39_afni_tiny/bin:/Users/nicolasambuco/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:/Library/Apple/usr/bin:/Users/nicolasambuco/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/X11/bin:/Users/nicolasambuco/abin
PYTHONPATH =
R_LIBS = /Users/nicolasambuco/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 = py39_afni_tiny
CC =
HOMEBREW_PREFIX = /opt/homebrew
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 2 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 0 0
.tcshrc 0 0 0 1
.profile 1 0 1 0
------------------------------ 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/nicolasambuco/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.5.4
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-1700.0.13.5)
brew gcc(s) : /opt/homebrew/bin/gcc-15
CommandLineTools SDK : MacOSX15.5.sdk
========================= summary, please fix: =========================
* just be aware: login shell 'sh', but our code examples use 'tcsh'
* shell sh : MISSING login shell setup file .profile
* dot file test : want 2 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)