AFNI showing different(abnormal) screen when I login and run afni .. for other users its normal.

AFNI showing different screen ( please check first image) only for my login. Its pulling some screen from somewhere and showing.

When I login and run afni for Other Users its normal ( please check the second image). I can see afni with all brain related images.

For all users — -check_all is SAME. Please help me.

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.1.2.el7.x86_64
version: #1 SMP Mon Sep 16 14:19:51 EDT 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/afni
afni version : Precompiled binary linux_openmp_64: Mar 12 2020
: AFNI_20.0.19 ‘Galba’
AFNI_version.txt : AFNI_20.0.19, linux_openmp_64, Mar 12 2020
which python : /bin/python
python version : 2.7.5
which R : /bin/R
R version : R version 3.6.0 (2019-04-26) – “Planting of a Tree”
which tcsh : /bin/tcsh

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

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success

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

R RHOME : /usr/lib64/R

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib64/python2.7/site-packages/PyQt4/init.pyc

** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /usr/bin/anaconda3/condabin:/usr/lib64/qt-3.3/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/local/afni:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/home/shiva/.local/bin:/home/shiva/bin:/usr/local/afni:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/home/shiva/.local/bin:/home/shiva/bin:/usr/local/afni:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/home/shiva/.local/bin:/home/shiva/bin:/usr/local/afni:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin

R_LIBS = /usr/local/R


------------------------------ 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/afni

------------------------------ OS specific -------------------------------
which yum : /bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • insufficient data for AFNI bootcamp


When you run “afni” in a terminal, the GUI will look for datasets in the present working directory (and potentially other locations, if you have environment variables set to do so). If it doesn’t find any datasets in the present directory, it will look in subdirectories, as well as in the same directory as the GUI itself. The GUI can open both neuroimaging datasets (.nii.gz or BRIK/HEAD files), as well as image files (.jpgs, for example). My guess is that in your present directory where you ran AFNI, you have no real neuroimaging datasets, but you do have a .jpg file-- and that is what AFNI has opened as an “axial” image. Or, do you have a file called "zyxt+orig" sitting in your present directory, somehow? Does running either of these in the directory where you are running your “odd result” AFNI show anything:

ls *jpg


ls zyxt*


Other people probably don’t have that specific file in the location where they ran AFNI, hence they don’t see that same “oddness”; the GUI searches in their location where “afni” itself is on their computer, which appears to be /usr/local/afni/.


Hi Taylor,

Thank you for your explanation. I will check them.

Hi Taylor

I installed afni under /usr/local/afni

With my login … if go to this directory path /usr/local/afni and run afni…

[shiva@localhost ~] cd /usr/local/afni

and run afni here like

[shiva@localhost afni] afni ---- then Its showing up the normal afni screen

But If I come out of the path (/usr/local/afni) … and run afni under $HOME like

[shiva@localhost ~] afni

then … I can see that GUI “oddness”.


OK, that all makes sense. The AFNI GUI is primarily used to look at datasets—if you have no datasets around, then what you are seeing can be expected to happen.

One place you can get datasets would be, for example, the AFNI Bootcamp data. This can be downloaded and opened in your home directory, as described here:
You could then go into any of those directories where datasets are (files ending with BRIK, HEAD, nii and/or nii.gz), and you should be able to view those fine.