conda issues with @auto_tlrc

Installation Issues
,
1

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)
2

Hi Nicola,

I suspect there is a problem with your .cshrc file (or .tcshrc file).
For example, open a new terminal window, and simply start a new tcsh.

tcsh

Does that fail out with similar errors?
If you would like me to look at your dot files, please run:

afni_system_check.py -dot_file_pack nicola_files.tgz

And then mail that tgz file to afni dot bootcamp at gmail dot com (as with our bootcamp setup).
Just let me know if that is not clear.
-rick

3

Thanks Rick, I'll send the compressed file via email shortly.
you're right tho: I also get error messages when I type 'tcsh' in a new terminal.
Any help would be very appreciated.

Nicola

4

Hi Nicola,

Thanks. You have a bunch of things in both the .cshrc and .tcshrc files, which might get confusing. With your setup, the .cshrc file is being processed first.

What is the output from:

ls -l ~/miniconda3/etc/profile.d/conda.csh

You might comment out the conda command on line 4 of your ~/.cshrc file, and see if just starting a new tcsh happens without errors.

-rick

5

Hi, I commented out line 4 of the ~/.cshrc file, but I'm still getting the same error for now.

The output that I got from your command is the following:
-rw-r--r-- 1 nicolasambuco staff 356 Jun 19 13:58 /Users/nicolasambuco/miniconda3/etc/profile.d/conda.cs

Thanks,
Nicola

6

Hi Nicola,

Sorry for letting this drop, I have been out for quite a while.

If this is still an issue, please let me know and we can resolve it.

-rick