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  

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February 07, 2021 05:02AM
Hi,

I'm using AFNI for a quite some time now and never had a problem launching the GUI. Just updated the XQuartz and AFNI won't launch, says the AFNI is detached from the terminal. Those are the outputs of the 'afni' command and afni_system_check.py -check_all:

[suntsmabookpro1:~/abin] sunt% afni
Precompiled binary macos_10.12_local: Jan 26 2021 (Version AFNI_21.0.06 'Titus')


** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to LR Frank for useful feedback

Initializing: X11++ AFNI is detached from terminal.



[suntsmabookpro1:~/abin] sunt% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              20.3.0
version:              Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64
distribution:         10.16
number of CPUs:       16
apparent login shell: tcsh
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/sunt/abin/afni
afni version         : Precompiled binary macos_10.12_local: Jan 26 2021 
                     : AFNI_21.0.06 'Titus'
AFNI_version.txt     : AFNI_21.0.06, macos_10.12_local, Jan 26 2021
which python         : /usr/bin/python
python version       : 2.7.16
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/sunt/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
    python  : 1   (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    python2 : 1   (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    python3 : 2 
      /usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
      /usr/bin/python3


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

++ module loaded: matplotlib.pyplot
   module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-- python binaries under /usr/local/bin:
    /usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
    /usr/local/bin/python3.9 (sym link to /usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/bin/python3.9)

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/share/dotnet:/opt/X11/bin:/Library/Apple/usr/bin:/Users/sunt/abin

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = 

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME
           top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos   under $HOME
           top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
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    : found TT_N27+tlrc  under .

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.0_beta3

which brew           : /usr/local/bin/brew
brew version         : Homebrew 2.7.2

-- for PyQt4 under brew, consider running:
   brew install cartr/qt4/pyqt
-- 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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

=========================  nothing to fix, yay!  =========================

Thanks!
Subject Author Posted

AFNI detached from terminal

sunt February 07, 2021 05:02AM

Re: AFNI detached from terminal

Daniel Glen February 07, 2021 03:52PM

Re: AFNI detached from terminal

sunt February 08, 2021 04:33AM

Re: AFNI detached from terminal

Daniel Glen February 08, 2021 04:19PM

Re: AFNI detached from terminal

Shawn November 07, 2021 04:29AM

Re: AFNI detached from terminal

Daniel Glen November 07, 2021 01:10PM

Re: AFNI detached from terminal

Shawn November 07, 2021 08:12PM

Re: AFNI detached from terminal

Daniel Glen November 08, 2021 10:21AM

Re: AFNI detached from terminal

Shawn November 09, 2021 02:46AM

Re: AFNI detached from terminal

rick reynolds November 09, 2021 11:33AM

Re: AFNI detached from terminal

Daniel Glen November 09, 2021 02:49PM

Re: AFNI detached from terminal

Shawn November 10, 2021 08:41AM

Re: AFNI detached from terminal

Daniel Glen November 10, 2021 03:28PM

Re: AFNI detached from terminal

Shawn November 11, 2021 08:33PM

Re: AFNI detached from terminal

Shawn November 10, 2021 08:35AM