AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
April 18, 2022 05:04PM
yes, I have python installed via miniconda3

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              21.4.0
version:              Darwin Kernel Version 21.4.0: Mon Feb 21 20:34:37 PST 2022; root:xnu-8020.101.4~2/RELEASE_X86_64
distribution:         10.16
number of CPUs:       6
apparent login shell: zsh
shell RC file:        .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/andrewlynn/abin/afni
afni version         : Precompiled binary macos_10.12_local: Dec  3 2021 
                     : AFNI_21.3.10 'Trajan'
AFNI_version.txt     : AFNI_21.3.10, macos_10.12_local, Dec 03 2021
which python         : /Users/andrewlynn/miniconda3/bin/python
python version       : 3.9.7
which R              : /usr/local/bin/R
R version            : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/andrewlynn/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
    python  : 1   (/Users/andrewlynn/miniconda3/bin/python3.9)
    python2 : 0 
    python3 : 3 
      /Users/andrewlynn/miniconda3/bin/python3.9
      /Library/Frameworks/Python.framework/Versions/3.10/bin/python3.10
      /usr/bin/python3

** have python3 but not python2

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /Library/Frameworks/R.framework/Resources

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-- python binaries under /usr/local/bin:
    /usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.10/bin/python3.10)
    /usr/local/bin/python3.9 (sym link to /usr/local/Cellar/python@3.9/3.9.6/Frameworks/Python.framework/Versions/3.9/bin/python3.9)

-------------------------------- env vars --------------------------------
PATH = /Users/andrewlynn/miniconda3/bin:/Users/andrewlynn/miniconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.10/bin:/Applications/freesurfer/7.1.1/bin:/Applications/freesurfer/7.1.1/fsfast/bin:/Applications/freesurfer/7.1.1/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/andrewlynn/abin

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
zsh compinit: insecure directories, run compaudit for list.
Ignore insecure directories and continue [y] or abort compinit [n]? y
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
zsh compinit: insecure directories, run compaudit for list.
Ignore insecure directories and continue [y] or abort compinit [n]? DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = 

------------------------------ 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/andrewlynn/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.1

which brew           : /usr/local/bin/brew
brew version         : Homebrew 3.2.7

++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /Users/andrewlynn/miniconda3/bin/python
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
   -- found 'libXt' dylib files:
      /opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'zsh'...
zsh compinit: insecure directories, run compaudit for list.
Ignore insecure directories and continue [y] or abort compinit [n]? y
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace

=========================  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)
*  please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh
Subject Author Posted

calling afni python scrips through MATLAB

aclynn11 April 18, 2022 03:31PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 04:16PM

Re: calling afni python scrips through MATLAB

Daniel Glen April 18, 2022 04:24PM

Re: calling afni python scrips through MATLAB

aclynn11 April 18, 2022 04:48PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 05:01PM

Re: calling afni python scrips through MATLAB

aclynn11 April 18, 2022 05:04PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 05:16PM

Re: calling afni python scrips through MATLAB

aclynn11 April 18, 2022 05:08PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 05:17PM