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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September 17, 2018 10:23AM
Hi I have installed afni in ubuntu 18 and the afni_system_check.py -check_all script is giving me some errors:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.15.0-34-generic
version: #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018
distribution: debian buster/sid
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/vicente/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 12 2018
: AFNI_18.2.16
AFNI_version.txt : AFNI_18.2.16, linux_ubuntu_16_64, Sep 12 2018
which python : /home/vicente/anaconda3/bin/python
python version : 2.7.15
which R : /usr/bin/R
R version : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/vicente/abin/afni)
R : 1 (/usr/bin/R)
python : 2
/home/vicente/anaconda3/bin/python2.7
/usr/bin/python2.7
python2 : 2
/home/vicente/anaconda3/bin/python2.7
/usr/bin/python2.7
python3 : 1 (/usr/bin/python3.6)


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
SurfMesh : success
3dClustSim : success

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

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

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /home/vicente/anaconda3/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/antsbin/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/home/vicente/anaconda3/bin:/usr/local/fsl/bin:/home/vicente/bin:/home/vicente/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/MATLAB/R2018a/bin/:/home/vicente/bin:/home/vicente/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/vicente/abin

PYTHONPATH =
R_LIBS = /home/vicente/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
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 /home/vicente/abin

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.3ubuntu0.1 (amd64)


========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate from 'tcsh'
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
Do you know how could i solve the AFNI programs falilure?
Subject Author Posted

afni_system_check.py -check_all problems

vferrer September 17, 2018 10:23AM

Re: afni_system_check.py -check_all problems

ptaylor September 17, 2018 11:04AM