Hi Daniel,

In short, I'm using Ubuntu 19.04, and the afni version Precompiled binary linux_ubuntu_16_64: Mar 8 2019 : AFNI_19.0.24 'Tiberius'

Just in case you want all the details, I have it here.

Also, if it took you too much time, and there was no apparently stupid bug in my code, feel free to ignore my report. After all you won't have to save images often for one study, and the codes sometimes work well.



Many thanks!!!

best,
Mengxing

The OS on which it does not work well (after it, you will find the system_check info for another OS that I tested on which the codes worked perfectly):
mengxing@XPS:~/.../01_Data_Analysis/GUI$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.15.0-1036-oem
version: #41-Ubuntu SMP Sun Apr 7 05:24:01 UTC 2019
distribution: Ubuntu 19.04 disco
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/mengxing/Application/afni/afni
afni version : Precompiled binary linux_ubuntu_16_64: Mar 8 2019
: AFNI_19.0.24 'Tiberius'
AFNI_version.txt : AFNI_19.0.24, linux_ubuntu_16_64, Mar 08 2019
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/bin/R
R version : R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/mengxing/Application/afni/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.7)


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : 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: snow!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!


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

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /home/mengxing/Application/freesurfer/bin:/home/mengxing/Application/freesurfer/fsfast/bin:/home/mengxing/Application/freesurfer/tktools:/home/mengxing/Application/freesurfer/mni/bin:/home/mengxing/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/mengxing/Application/afni:/home/mengxing/Application/afni

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...9 [ptaylor]: added FT_analysis/results.QC_FT.05 tree
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/mengxing/Application/afni

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.8.0 (amd64)

have Ubuntu system: Ubuntu 19.04 disco
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Mar 8 2019

========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .profile
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp

----------------------------------------------------------------------------------------------------------------------------------

The other OS that it worked well:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-862.3.2.el7.x86_64
version: #1 SMP Mon May 21 23:36:36 UTC 2018
distribution: CentOS Linux 7.5.1804 Core
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)


--------------------- AFNI and related program tests ---------------------
which afni : /opt/afni/linux_openmp_64/afni
afni version : Precompiled binary linux_openmp_64: Feb 4 2019
: AFNI_19.0.06 'Tiberius'
AFNI_version.txt : AFNI_19.0.06, linux_openmp_64, Feb 04 2019
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/bin/R
R version : R version 3.5.0 (2018-04-23) -- "Joy in Playing"
which tcsh : /usr/bin/tcsh


instances of various programs found in PATH:
afni : 2
/opt/afni/linux_openmp_64/afni
/opt/afni-stable/linux_openmp_64/afni
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 0




testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success


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


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


------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4


-------------------------------- env vars --------------------------------
PATH = /opt/afni/linux_openmp_64:/opt/afni-stable/linux_openmp_64:/opt/Modules/bin:/opt/dtk:/opt/workbench/bin_rh_linux64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/export/home/lmengxing/.local/bin:/export/home/lmengxing/bin


PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/lib


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 /opt/afni/linux_openmp_64


------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 0.6.4
which yum : /usr/bin/yum
yum version : 3.4.3




========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* have multiple versions of AFNI in PATH
* consider running: cp /opt/afni/linux_openmp_64/AFNI.afnirc ~/.afnirc
* consider running: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp



Thanks!!