Hello - I've had AFNI working on my Mac (M3, Sonoma) for a few months now, including a post-processing custom script that uses 3dNwarpXYZ to transform tlrc coordinates in 1D files into orig coordinates.
Now, we are getting an error with 3dNwarpXYZ saying that it cannot read the 1D files. I have confirmed that the file exists, and that I have full read/write/execute access to the 1D file.
Is there a specific python/R package that 3dNWarpXYZ uses that may have gone missing?
Output from afni_system_check.py -check_all :
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.2.0
version: Darwin Kernel Version 23.2.0: Wed Nov 15 21:54:55 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T8122
distribution: 14.2.1
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/hml/abin/afni
afni version : Precompiled binary macos_13_ARM_clang: May 24 2024
: AFNI_24.1.10 'Publius Septimius Geta'
AFNI_version.txt : AFNI_24.1.10, macos_13_ARM_clang, May 24 2024, build
which python : /Users/hml/.pyenv/versions/3.11.9/bin/python
python version : 3.11.9
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)
instances of various programs found in PATH:
afni : 1 (/Users/hml/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 3
/Users/hml/.pyenv/versions/3.11.9/bin/python3.11
/Users/hml/.pyenv/shims/python
/usr/bin/python3
python2 : 0
python3 : 3
/Users/hml/.pyenv/versions/3.11.9/bin/python3.11
/Users/hml/.pyenv/shims/python3
/usr/bin/python3
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : 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/hml/.pyenv/versions/3.11.9/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.9.0
** 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/python (sym link to /usr/bin/python3)
-------------------------------- env vars --------------------------------
PATH = /Users/hml/.pyenv/versions/3.11.9/bin:/opt/homebrew/Cellar/pyenv/2.4.1/libexec:/opt/homebrew/Cellar/pyenv/2.4.1/plugins/python-build/bin:/Users/hml/.pyenv/shims:/opt/homebrew/bin:/opt/homebrew/sbin:/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:/usr/local/munki:/Users/hml/Applications/SimNIBS-4.0/bin:/opt/homebrew/opt/python/libexec/bin:/Users/hml/abin
PYTHONPATH =
R_LIBS = /Users/hml/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
----------------------------- 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)
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 : found TT_N27+tlrc under /Users/hml/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.3.1
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)