afni/suma not available to system wide users in RHEL 7

I installed afni/suma and R as a root use and set the path in /etc.profile.d for system wide access to users.

When I logged into as another USER and run afni command not found message.

[shiva@localhost ~] afni
afni: command not found message

this is my afni system check. Please help me how to fix it. -check_all
-------------------------------- 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 : /root/abin/afni
afni version : Precompiled binary linux_centos_7_64: Feb 3 2020
: AFNI_20.0.05 ‘Galba’
AFNI_version.txt : AFNI_20.0.05, linux_centos_7_64, Feb 03 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 (/root/abin/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/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/root/abin:/usr/bin/R:/home/shivaram/.local/bin:/home/shivaram/bin:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/root/abin:/usr/bin/R:/home/shivaram/.local/bin:/home/shivaram/bin:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/root/abin:/usr/bin/R:/home/shivaram/.local/bin:/home/shivaram/bin:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin:/root/abin:/usr/bin/R:/usr/bin/anaconda3/bin:/usr/bin/anaconda3/condabin

R_LIBS = /root/R

LD_LIBRARY_PATH = /usr/lib/


------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under /home/shivaram
top history: …2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under /home/shivaram
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under /home/shivaram
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under /home/shivaram
atlas : found TT_N27+tlrc under /root/abin

------------------------------ 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’

I really don’t think it’s a good idea to put abin in /root/.

We would recommend following these instructions:

The system check shows /root/abin in your $PATH in several places, so it is possible you haven’t re-sourced your shell RC file (or opened a new terminal).


In particular, the /root directory is not generally even readable by any user other than root, so adding it to that user’s PATH is not enough. Move /root/abin to something like /usr/local/afnibin, for example. Then have users put that directory in their PATHs.

At that point, you might need to be sure that the abin (or /usr/local/afnibin) directories still have world read/execute access, too.

  • rick