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!
