Hi,
1). Running @chauffeur_afni -input DSET results in an error --
\@chauffeur_afni -ulay sub-055_ses-01_T1w.nii
++ My command:
@chauffeur_afni -ulay sub-055_ses-01_T1w.nii
** ERROR: Xvfb -- not found in path -- program fails
++ DONE (bad exit): check for errors
2) Here's my output of afni_system_check.py -check_all :
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 2.6.32-754.35.1.el6.x86_64
version: #1 SMP Wed Sep 16 06:48:01 EDT 2020
distribution: Red Hat Enterprise Linux Server 6.10 Santiago
number of CPUs: 20
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /gpfs/group/dml129/default/sw/afni/20.1.13/bin/afni
afni version : Precompiled binary linux_openmp_64: Jun 4 2020
: AFNI_20.1.13 'Otho'
AFNI_version.txt : AFNI_20.1.13, linux_openmp_64, Jun 04 2020
which python : /opt/aci/sw/python/3.6.3_anaconda-5.0.1/bin/python
python version : 3.6.3
which R : /usr/bin/R
R version : R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/gpfs/group/dml129/default/sw/afni/20.1.13/bin/afni)
R : 1 (/usr/bin/R)
python : 2
/opt/aci/sw/python/3.6.3_anaconda-5.0.1/bin/python3.6
/usr/bin/python
python2 : 1 (/usr/bin/python)
python3 : 2
/opt/aci/sw/python/3.6.3_anaconda-5.0.1/bin/python3.6
/usr/bin/python3.4
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : 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: lmerTest!
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!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib64/R
checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /opt/aci/sw/python/3.6.3_anaconda-5.0.1/lib/python3.6/site-packages/matplotlib/pyplot.py
-------------------------------- env vars --------------------------------
PATH = storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:/gpfs/group/dml129/default/sw/afni/20.1.13/bin:/opt/aci/sw/python/3.6.3_anaconda-5.0.1/scripts:/opt/aci/sw/python/3.6.3_anaconda-5.0.1/bin:/usr/local/bin:/usr/local/sbin:storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/local/moab/bin:/usr/local/bin:/usr/local/sbin:storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/opt/TurboVNC/bin:storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:storage/home/cfg2/.local/bin:/gpfs/group/cfg2/default/sw/freesurfer/bin:/gpfs/group/cfg2/default/sw/freesurfer/fsfast/bin:/gpfs/group/cfg2/default/sw/freesurfer/tktools:/gpfs/group/cfg2/default/sw/freesurfer/mni/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/local/sbin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/opt/puppetlabs/bin:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab:/storage/home/cfg2/bin:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab:/opt/puppetlabs/bin:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab:/storage/work/cfg2/dcm2niix/build/bin:/storage/work/cfg2/r_packages:/storage/home/cfg2/work/chuck_scripts:/gpfs/group/cfg2/default/projects/ahab
PYTHONPATH = /opt/aci/sw/python/3.6.3_anaconda-5.0.1/lib
R_LIBS =
LD_LIBRARY_PATH = /opt/aci/sw/python/3.6.3_anaconda-5.0.1/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 /gpfs/group/dml129/default/sw/afni/20.1.13/bin
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.2.29
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* have python version 3.6.3, some programs need 2.7.x
* missing R packages (see rPkgsInstall)
* please run: cp /gpfs/group/dml129/default/sw/afni/20.1.13/bin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
