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March 07, 2022 10:54AM
Hi,
I have recently downloaded AFNI on my desktop (Windows 10) using the ‘Quick Setup’ instructions here (after having downloaded Linux and XQuartz): [afni.nimh.nih.gov]
However, I am unable to open AFNI through the Ubuntu terminal. I get the following error message when I type “afni”:

Precompiled binary linux_ubuntu_16_64: Feb 18 2022 (Version AFNI_22.0.11 'Hadrian')

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to P Kundu for great efforts

Initializing: X11Error: Can't open display: :0.0
++ AFNI is detached from terminal.


This is the message I get following the command “afni_system_check.py -check_all”:

-------------------------------- general ---------------------------------
architecture:         64bit ELF
system:               Linux
release:              5.10.16.3-microsoft-standard-WSL2
version:              #1 SMP Fri Apr 2 22:23:49 UTC 2021
distribution:         ubuntu 20.04 focal
number of CPUs:       6
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/marcus/abin/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Feb 18 2022
                     : AFNI_22.0.11 'Hadrian'
AFNI_version.txt     : AFNI_22.0.11, linux_ubuntu_16_64, Feb 18 2022
which python         : /usr/bin/python
python version       : 3.8.2
which R              : /usr/bin/R
R version            : R version 4.1.2 (2021-11-01) -- "Bird Hippie"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/home/marcus/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.8)
    python2 : 0
    python3 : 1   (/usr/bin/python3.8)

** 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 : FAILURE

        oo Warning:
           These packages are not installed on the computer: afex!
        These packages are not installed on the computer: phia!
        These packages are not installed on the computer: lmerTest!


R RHOME : /usr/lib/R

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 : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
   matplotlib version : 3.1.2

-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.UbuntuonWindows_2004.2020.424.0_x64__79rhkp1fndgsc:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Windows/System32/OpenSSH/:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/d/Program Files/MATLAB/R2020b/bin:/mnt/c/Program Files/PsychoPy3:/mnt/c/Program Files/PsychoPy3/DLLs:/mnt/c/Program Files/dotnet/:/mnt/c/Users/Marcus/AppData/Local/Programs/Python/Python39/Scripts/:/mnt/c/Users/Marcus/AppData/Local/Programs/Python/Python39/:/mnt/c/Users/Marcus/AppData/Local/Microsoft/WindowsApps:/snap/bin:/home/marcus/abin

PYTHONPATH =
R_LIBS = /home/marcus/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME (257007M Avail)
           top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos   under $HOME
           top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_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 /home/marcus/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.0.2 (amd64)

have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Feb 18 2022

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  missing R packages (see rPkgsInstall)

Any ideas on how to fix this? I have seen similar questions posted before, but they all appear to have slightly different issues.
Thank you very much for your time!
Subject Author Posted

AFNI Opening Issue - "AFNI is detached from terminal"

MarcusG March 07, 2022 10:54AM

Re: AFNI Opening Issue - "AFNI is detached from terminal"

Daniel Glen March 07, 2022 02:29PM

Re: AFNI Opening Issue - "AFNI is detached from terminal"

MarcusG April 07, 2022 06:57AM

Re: AFNI Opening Issue - "AFNI is detached from terminal"

Daniel Glen April 07, 2022 10:04AM

Re: AFNI Opening Issue - "AFNI is detached from terminal"

MarcusG April 12, 2022 09:49AM



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