AFNI version info (afni -ver):
AFNI_23.1.10, conda_centos7_64, Jul 08 2023, conda-build
Hi,
I'm trying to run 3dLMEr on a longitudinal dataset. You can see the model specification below. I use afni on a cluster from my university so any changes you suggest I cannot make them, but can let them know.
3dLMEr -prefix /path//results_3dLMEr_ECN.nii -jobs 8 \
-mask /path/ECN_mask.nii \
-model 'session+age+sex+FD+(FD|Subj)' \
-resid /path/residuals_3dLMEr_ECN.nii \
-qVars 'age,FD' \
-dataTable \
Subj session age sex FD InputFile \
sub-patient01 ses-01 1 25 0.1907 /path/connmap_sub-patient01_ses-01_ECN.nii \
sub-patient01 ses-02 1 25 0.25926 /path/connmap_sub-patient01_ses-02_ECN.nii \
sub-patient01 ses-03 1 25 0.23718 /path/connmap_sub-patient01_ses-03_ECN.nii \
sub-patient02 ses-02 0 30 0.19278 /path/connmap_sub-patient02_ses-02_ECN.nii \
sub-patient03 ses-01 0 28 0.13903 /path/connmap_sub-patient03_ses-01_ECN.nii \
This is the error that I get after running tcsh -x 3dLMEr.txt
* Error:
Missing R_io.so
Error in if (an$type == "BRIK" && !is.na(an$view)) { :
missing value where TRUE/FALSE needed
Calls: process.LME.opts -> exists.AFNI.name -> file.exists -> head.AFNI.name
Execution halted
After reading some previous posts, it was recommended to run afni_system_check.py -check_all. This is my output:
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 3.10.0-1160.24.1.el7.x86_64
version: #1 SMP Thu Mar 25 21:21:56 UTC 2021
distribution: rhel 7.9 Maipo
number of CPUs: 5
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/omaximo/.conda/envs/afni23/bin/afni
afni version : afni: error while loading shared libraries: libjpeg.so.9: cannot open shared object file: No such file or directory
:
AFNI_version.txt : AFNI_23.1.10, conda_centos7_64, Jul 08 2023, conda-build
which python : /home/omaximo/.conda/envs/afni23/bin/python
python version : 3.10.18
which R : /home/omaximo/.conda/envs/afni23/bin/R
R version : R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
instances of various programs found in PATH:
afni : 1 (/home/omaximo/.conda/envs/afni23/bin/afni)
R : 2
/home/omaximo/.conda/envs/afni23/bin/R
/share/apps/rc/software/R/4.3.2-gfbf-2023a/bin/R
python : 4
/home/omaximo/.conda/envs/afni23/bin/python3.10
/share/apps/rc/software/Anaconda3/2023.07-2/bin/python3.11
/share/apps/rc/software/Python/3.11.3-GCCcore-12.3.0/bin/python3.11
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 4
/home/omaximo/.conda/envs/afni23/bin/python3.10
/share/apps/rc/software/Anaconda3/2023.07-2/bin/python3.11
/share/apps/rc/software/Python/3.11.3-GCCcore-12.3.0/bin/python3.11
/usr/bin/python3.6
testing ability to start various programs...
afni : FAILURE
afni: error while loading shared libraries: libjpeg.so.9: cannot open shared object file: No such file or directory
suma : FAILURE
suma: error while loading shared libraries: libjpeg.so.9: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libjpeg.so.9: cannot open shared object file: No such file or directory
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libjpeg.so.9: cannot open shared object file: No such file or directory
3dClustSim : success
uber_subject.py : success
3dMVM : success
** missing binary library 'libjpeg.so.9' across 4 programs
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /share/apps/rc/software/tcsh/6.24.10-GCCcore-12.3.0/bin/tcsh
which Xvfb : /share/apps/rc/software/Xvfb/21.1.8-GCCcore-12.3.0/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /home/omaximo/.conda/envs/afni23/lib/R
------------------------------ python libs -------------------------------
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
-------------------------------- env vars --------------------------------
PATH = /home/omaximo/.conda/envs/afni23/bin:/share/apps/rc/software/Anaconda3/2023.07-2/condabin:/share/apps/rc/software/Anaconda3/2023.07-2/bin:/share/apps/rc/software/FFmpeg/6.0-GCCcore-12.3.0/bin:/share/apps/rc/software/SDL2/2.28.2-GCCcore-12.3.0/bin:/share/apps/rc/software/x265/3.5-GCCcore-12.3.0/bin:/share/apps/rc/software/LAME/3.100-GCCcore-12.3.0/bin:/share/apps/rc/software/x264/20230226-GCCcore-12.3.0/bin:/share/apps/rc/software/Xvfb/21.1.8-GCCcore-12.3.0/bin:/share/apps/rc/software/nettle/3.9.1-GCCcore-12.3.0/bin:/share/apps/rc/software/matplotlib/3.7.2-gfbf-2023a/bin:/share/apps/rc/software/Qhull/2020.2-GCCcore-12.3.0/bin:/share/apps/rc/software/SciPy-bundle/2023.07-gfbf-2023a/bin:/share/apps/rc/software/pybind11/2.11.1-GCCcore-12.3.0/bin:/share/apps/rc/software/Python-bundle-PyPI/2023.06-GCCcore-12.3.0/bin:/share/apps/rc/software/virtualenv/20.23.1-GCCcore-12.3.0/bin:/share/apps/rc/software/LittleCMS/2.15-GCCcore-12.3.0/bin:/share/apps/rc/software/OpenJPEG/2.5.0-GCCcore-12.3.0/bin:/share/apps/rc/software/libwebp/1.3.1-GCCcore-12.3.0/bin:/share/apps/rc/software/giflib/5.2.1-GCCcore-12.3.0/bin:/share/apps/rc/software/GSL/2.7-GCC-12.3.0/bin:/share/apps/rc/software/PyQt5/5.15.10-GCCcore-12.3.0/bin:/share/apps/rc/software/Qt5/5.15.10-GCCcore-12.3.0/bin:/share/apps/rc/software/nodejs/18.17.1-GCCcore-12.3.0/bin:/share/apps/rc/software/JasPer/4.0.0-GCCcore-12.3.0/bin:/share/apps/rc/software/NSS/3.89.1-GCCcore-12.3.0/bin:/share/apps/rc/software/NSPR/4.35-GCCcore-12.3.0/bin:/share/apps/rc/software/DBus/1.15.4-GCCcore-12.3.0/bin:/share/apps/rc/software/graphite2/1.3.14-GCCcore-12.3.0/bin:/share/apps/rc/software/R/4.3.2-gfbf-2023a/bin:/share/apps/rc/software/FriBidi/1.0.12-GCCcore-12.3.0/bin:/share/apps/rc/software/HarfBuzz/5.3.1-GCCcore-12.3.0/bin:/share/apps/rc/software/ICU/73.2-GCCcore-12.3.0/sbin:/share/apps/rc/software/ICU/73.2-GCCcore-12.3.0/bin:/share/apps/rc/software/Tk/8.6.13-GCCcore-12.3.0/bin:/share/apps/rc/software/cURL/8.0.1-GCCcore-12.3.0/bin:/share/apps/rc/software/libgit2/1.7.1-GCCcore-12.3.0/bin:/share/apps/rc/software/PCRE/8.45-GCCcore-12.3.0/bin:/share/apps/rc/software/Java/11.0.2:/share/apps/rc/software/Java/11.0.2/bin:/share/apps/rc/software/LibTIFF/4.5.0-GCCcore-12.3.0/bin:/share/apps/rc/software/libdeflate/1.18-GCCcore-12.3.0/bin:/share/apps/rc/software/jbigkit/2.1-GCCcore-12.3.0/bin:/share/apps/rc/software/cairo/1.17.8-GCCcore-12.3.0/bin:/share/apps/rc/software/GLib/2.77.1-GCCcore-12.3.0/bin:/share/apps/rc/software/PCRE2/10.42-GCCcore-12.3.0/bin:/share/apps/rc/software/gettext/0.21.1-GCCcore-12.3.0/bin:/share/apps/rc/software/LLVM/16.0.6-GCCcore-12.3.0/bin:/share/apps/rc/software/zstd/1.5.5-GCCcore-12.3.0/bin:/share/apps/rc/software/lz4/1.9.4-GCCcore-12.3.0/bin:/share/apps/rc/software/gzip/1.12-GCCcore-12.3.0/bin:/share/apps/rc/software/motif/2.3.8-GCCcore-12.3.0/bin:/share/apps/rc/software/libjpeg-turbo/2.1.5.1-GCCcore-12.3.0/bin:/share/apps/rc/software/NASM/2.16.01-GCCcore-12.3.0/bin:/share/apps/rc/software/X11/20230603-GCCcore-12.3.0/bin:/share/apps/rc/software/fontconfig/2.14.2-GCCcore-12.3.0/bin:/share/apps/rc/software/util-linux/2.39-GCCcore-12.3.0/sbin:/share/apps/rc/software/util-linux/2.39-GCCcore-12.3.0/bin:/share/apps/rc/software/freetype/2.13.0-GCCcore-12.3.0/bin:/share/apps/rc/software/Brotli/1.0.9-GCCcore-12.3.0/bin:/share/apps/rc/software/libpng/1.6.39-GCCcore-12.3.0/bin:/share/apps/rc/software/expat/2.5.0-GCCcore-12.3.0/bin:/share/apps/rc/software/Python/3.11.3-GCCcore-12.3.0/bin:/share/apps/rc/software/SQLite/3.42.0-GCCcore-12.3.0/bin:/share/apps/rc/software/Tcl/8.6.13-GCCcore-12.3.0/bin:/share/apps/rc/software/bzip2/1.0.8-GCCcore-12.3.0/bin:/share/apps/rc/software/tcsh/6.24.10-GCCcore-12.3.0/bin:/share/apps/rc/software/ncurses/6.4-GCCcore-12.3.0/bin:/share/apps/rc/software/FFTW/3.3.10-GCC-12.3.0/bin:/share/apps/rc/software/FlexiBLAS/3.3.1-GCC-12.3.0/bin:/share/apps/rc/software/OpenMPI/4.1.5-GCC-12.3.0/bin:/share/apps/rc/software/UCC/1.2.0-GCCcore-12.3.0/bin:/share/apps/rc/software/PMIx/4.2.4-GCCcore-12.3.0/bin:/share/apps/rc/software/libfabric/1.18.0-GCCcore-12.3.0/bin:/share/apps/rc/software/UCX/1.14.1-GCCcore-12.3.0/bin:/share/apps/rc/software/libevent/2.1.12-GCCcore-12.3.0/bin:/share/apps/rc/software/OpenSSL/1.1/bin:/share/apps/rc/software/hwloc/2.9.1-GCCcore-12.3.0/sbin:/share/apps/rc/software/hwloc/2.9.1-GCCcore-12.3.0/bin:/share/apps/rc/software/libxml2/2.11.4-GCCcore-12.3.0/bin:/share/apps/rc/software/XZ/5.4.2-GCCcore-12.3.0/bin:/share/apps/rc/software/numactl/2.0.16-GCCcore-12.3.0/bin:/share/apps/rc/software/binutils/2.40-GCCcore-12.3.0/bin:/share/apps/rc/software/GCCcore/12.3.0/bin:/cm/shared/apps/slurm/18.08.9/sbin:/cm/shared/apps/slurm/18.08.9/bin:/share/apps/rc/bin:/opt/TurboVNC/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/home/omaximo/scripts:/data/project/lahtilab/beest/containers
PYTHONPATH = /share/apps/rc/software/matplotlib/3.7.2-gfbf-2023a/lib/python3.11/site-packages:/share/apps/rc/software/Tkinter/3.11.3-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages:/share/apps/rc/software/pybind11/2.11.1-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/Python-bundle-PyPI/2023.06-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/virtualenv/20.23.1-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/cryptography/41.0.1-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/cffi/1.15.1-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/Pillow/10.0.0-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/PyQt5/5.15.10-GCCcore-12.3.0/lib/python3.11/site-packages:/share/apps/rc/software/Python/3.11.3-GCCcore-12.3.0/easybuild/python
R_LIBS = /home/omaximo/.conda/envs/afni23/lib/R/library
LD_LIBRARY_PATH = /share/apps/rc/software/FFmpeg/6.0-GCCcore-12.3.0/lib:/share/apps/rc/software/SDL2/2.28.2-GCCcore-12.3.0/lib:/share/apps/rc/software/x265/3.5-GCCcore-12.3.0/lib:/share/apps/rc/software/LAME/3.100-GCCcore-12.3.0/lib:/share/apps/rc/software/x264/20230226-GCCcore-12.3.0/lib:/share/apps/rc/software/Xvfb/21.1.8-GCCcore-12.3.0/lib:/share/apps/rc/software/nettle/3.9.1-GCCcore-12.3.0/lib:/share/apps/rc/software/GMP/6.2.1-GCCcore-12.3.0/lib:/share/apps/rc/software/Qhull/2020.2-GCCcore-12.3.0/lib:/share/apps/rc/software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages/numpy/core/lib:/share/apps/rc/software/LittleCMS/2.15-GCCcore-12.3.0/lib:/share/apps/rc/software/OpenJPEG/2.5.0-GCCcore-12.3.0/lib:/share/apps/rc/software/libwebp/1.3.1-GCCcore-12.3.0/lib:/share/apps/rc/software/giflib/5.2.1-GCCcore-12.3.0/lib:/share/apps/rc/software/freeglut/3.4.0-GCCcore-12.3.0/lib:/share/apps/rc/software/GSL/2.7-GCC-12.3.0/lib:/share/apps/rc/software/Qt5/5.15.10-GCCcore-12.3.0/lib:/share/apps/rc/software/nodejs/18.17.1-GCCcore-12.3.0/lib:/share/apps/rc/software/JasPer/4.0.0-GCCcore-12.3.0/lib:/share/apps/rc/software/snappy/1.1.10-GCCcore-12.3.0/lib:/share/apps/rc/software/NSS/3.89.1-GCCcore-12.3.0/lib:/share/apps/rc/software/NSPR/4.35-GCCcore-12.3.0/lib:/share/apps/rc/software/DBus/1.15.4-GCCcore-12.3.0/lib:/share/apps/rc/software/graphite2/1.3.14-GCCcore-12.3.0/lib:/share/apps/rc/software/double-conversion/3.3.0-GCCcore-12.3.0/lib:/share/apps/rc/software/R/4.3.2-gfbf-2023a/lib/R/lib:/share/apps/rc/software/FriBidi/1.0.12-GCCcore-12.3.0/lib:/share/apps/rc/software/HarfBuzz/5.3.1-GCCcore-12.3.0/lib:/share/apps/rc/software/ICU/73.2-GCCcore-12.3.0/lib:/share/apps/rc/software/Tk/8.6.13-GCCcore-12.3.0/lib:/share/apps/rc/software/cURL/8.0.1-GCCcore-12.3.0/lib:/share/apps/rc/software/libgit2/1.7.1-GCCcore-12.3.0/lib:/share/apps/rc/software/PCRE/8.45-GCCcore-12.3.0/lib:/share/apps/rc/software/Java/11.0.2/lib:/share/apps/rc/software/LibTIFF/4.5.0-GCCcore-12.3.0/lib:/share/apps/rc/software/libdeflate/1.18-GCCcore-12.3.0/lib:/share/apps/rc/software/jbigkit/2.1-GCCcore-12.3.0/lib:/share/apps/rc/software/cairo/1.17.8-GCCcore-12.3.0/lib:/share/apps/rc/software/GLib/2.77.1-GCCcore-12.3.0/lib:/share/apps/rc/software/PCRE2/10.42-GCCcore-12.3.0/lib:/share/apps/rc/software/gettext/0.21.1-GCCcore-12.3.0/lib:/share/apps/rc/software/pixman/0.42.2-GCCcore-12.3.0/lib:/share/apps/rc/software/libGLU/9.0.3-GCCcore-12.3.0/lib:/share/apps/rc/software/Mesa/23.1.4-GCCcore-12.3.0/lib:/share/apps/rc/software/LLVM/16.0.6-GCCcore-12.3.0/lib:/share/apps/rc/software/libunwind/1.6.2-GCCcore-12.3.0/lib:/share/apps/rc/software/libglvnd/1.6.0-GCCcore-12.3.0/lib:/share/apps/rc/software/libdrm/2.4.115-GCCcore-12.3.0/lib:/share/apps/rc/software/zstd/1.5.5-GCCcore-12.3.0/lib:/share/apps/rc/software/lz4/1.9.4-GCCcore-12.3.0/lib:/share/apps/rc/software/motif/2.3.8-GCCcore-12.3.0/lib:/share/apps/rc/software/libjpeg-turbo/2.1.5.1-GCCcore-12.3.0/lib:/share/apps/rc/software/X11/20230603-GCCcore-12.3.0/lib:/share/apps/rc/software/fontconfig/2.14.2-GCCcore-12.3.0/lib:/share/apps/rc/software/util-linux/2.39-GCCcore-12.3.0/lib:/share/apps/rc/software/freetype/2.13.0-GCCcore-12.3.0/lib:/share/apps/rc/software/Brotli/1.0.9-GCCcore-12.3.0/lib:/share/apps/rc/software/libpng/1.6.39-GCCcore-12.3.0/lib:/share/apps/rc/software/expat/2.5.0-GCCcore-12.3.0/lib:/share/apps/rc/software/Python/3.11.3-GCCcore-12.3.0/lib:/share/apps/rc/software/libffi/3.4.4-GCCcore-12.3.0/lib64:/share/apps/rc/software/SQLite/3.42.0-GCCcore-12.3.0/lib:/share/apps/rc/software/Tcl/8.6.13-GCCcore-12.3.0/lib:/share/apps/rc/software/libreadline/8.2-GCCcore-12.3.0/lib:/share/apps/rc/software/bzip2/1.0.8-GCCcore-12.3.0/lib:/share/apps/rc/software/ncurses/6.4-GCCcore-12.3.0/lib:/share/apps/rc/software/ScaLAPACK/2.2.0-gompi-2023a-fb/lib:/share/apps/rc/software/FFTW.MPI/3.3.10-gompi-2023a/lib:/share/apps/rc/software/FFTW/3.3.10-GCC-12.3.0/lib:/share/apps/rc/software/FlexiBLAS/3.3.1-GCC-12.3.0/lib:/share/apps/rc/software/OpenBLAS/0.3.23-GCC-12.3.0/lib:/share/apps/rc/software/OpenMPI/4.1.5-GCC-12.3.0/lib:/share/apps/rc/software/UCC/1.2.0-GCCcore-12.3.0/lib:/share/apps/rc/software/PMIx/4.2.4-GCCcore-12.3.0/lib:/share/apps/rc/software/libfabric/1.18.0-GCCcore-12.3.0/lib:/share/apps/rc/software/UCX/1.14.1-GCCcore-12.3.0/lib:/share/apps/rc/software/libevent/2.1.12-GCCcore-12.3.0/lib:/share/apps/rc/software/OpenSSL/1.1/lib:/share/apps/rc/software/hwloc/2.9.1-GCCcore-12.3.0/lib:/share/apps/rc/software/libpciaccess/0.17-GCCcore-12.3.0/lib:/share/apps/rc/software/libxml2/2.11.4-GCCcore-12.3.0/lib:/share/apps/rc/software/XZ/5.4.2-GCCcore-12.3.0/lib:/share/apps/rc/software/numactl/2.0.16-GCCcore-12.3.0/lib:/share/apps/rc/software/binutils/2.40-GCCcore-12.3.0/lib:/share/apps/rc/software/zlib/1.2.13-GCCcore-12.3.0/lib:/share/apps/rc/software/GCCcore/12.3.0/lib64:/cm/shared/apps/slurm/18.08.9/lib64/slurm:/cm/shared/apps/slurm/18.08.9/lib64
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- no .tcshrc, will create one as a follower of .cshrc
-- considered operations: path, flatdir, apsearch
(not on a mac, should skip flatdir)
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 4 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 1 0 1 0
.tcshrc 0 0 0 1
.bashrc 1 0 1 0
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
which yum : /bin/yum
yum version : There was a problem importing one of the Python modules
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing binary library: libjpeg.so.9
* python library matplotlib is required
(see AFNI install docs for details)
* please run: cp /home/omaximo/.conda/envs/afni23/bin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* dot file test : want 4 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* possibly missing atlases
Any suggestions?
Thank you.