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  

|
May 30, 2022 10:12AM
Thanks so much Rick!

Here's my output from cat /etc/os-release

tue50988@cla19097:~$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.4 LTS"
VERSION_ID="20.04"
HOME_URL="[www.ubuntu.com];
SUPPORT_URL="[help.ubuntu.com];
BUG_REPORT_URL="[bugs.launchpad.net];
PRIVACY_POLICY_URL="[www.ubuntu.com];
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal

and here's the output from: afni_system_check.py -check_all

tue50988@cla19097:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.13.0-44-generic
version: #49~20.04.1-Ubuntu SMP Wed May 18 18:44:28 UTC 2022
distribution: ubuntu 20.04 focal
number of CPUs: 48
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/abin/afni
afni version : /bin/sh: 1: afni: Exec format error
:
AFNI_version.txt : AFNI_22.1.10, macos_10.12_local, May 20 2022
which python : /usr/bin/python
python version : 3.8.10
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)


testing ability to start various programs...
afni : FAILURE
/bin/sh: 1: afni: Exec format error
suma : FAILURE
/bin/sh: 1: suma: Exec format error
3dSkullStrip : FAILURE
/bin/sh: 1: 3dSkullStrip: Exec format error
uber_subject.py : success
3dAllineate : FAILURE
/bin/sh: 1: 3dAllineate: Exec format error
3dRSFC : FAILURE
/bin/sh: 1: 3dRSFC: Exec format error
SurfMesh : FAILURE
/bin/sh: 1: SurfMesh: Exec format error
3dClustSim : FAILURE
/bin/sh: 1: 3dClustSim: Exec format error
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/usr/local/abin/R_io.so':
/usr/local/abin/R_io.so: invalid ELF header
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

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

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 = /home/local/TU/tue50988/.local/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/abin:/usr/local/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ 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 /usr/local/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.8 (amd64)

have Ubuntu system: ubuntu 20.04 focal

========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
Subject Author Posted

AFNI Install for Multiple users

MeganQ May 30, 2022 09:14AM

Re: AFNI Install for Multiple users

rick reynolds May 30, 2022 10:05AM

Re: AFNI Install for Multiple users

MeganQ May 30, 2022 10:12AM

Re: AFNI Install for Multiple users

rick reynolds May 30, 2022 08:36PM

Re: AFNI Install for Multiple users

MeganQ May 31, 2022 08:22AM