Error when running 3dMSS: "The content under -dataTable is not rectangular!"

rickr · September 10, 2024, 7:29pm

So tcsh is messed up, meaning there is some error in either .cshrc or .tcshrc.

I will send you a private message. You can run:

afni_system_check.py -dot_file_pack bad_tcsh.tgz

and I will include an email address that you can attach bad_tcsh.tgz to so that both Paul and I can see it.

rick

rickr · September 10, 2024, 8:21pm

Hello,
Thanks for the dot files.
Please edit your ~/.cshrc file, changing the first line to read:

set path = ( $path /software/afni/21.1.07 )

Then try the system check again:

afni_system_check.py -check_all

Thanks,

rick

ptaylor · September 10, 2024, 8:35pm

On a minor note, the export statement in line 14 ".bashrc" should also be updated to be:

export PATH=$PATH:/software/afni/21.1.07

(that is, don't have that final "afni" at the end, because that is the program name, not part of the directory path structure.)

--pt

cmahlen · September 10, 2024, 8:54pm

Running @SSwarper -help does not raise an error now! I will try using it and report back if there are any issues.

After following both of your suggestions, here is the output of afni_system_check:

[cmahlen@bhg0016 ses-bsl]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit ELF
system:               Linux
release:              3.10.0-1160.95.1.el7.x86_64
version:              #1 SMP Fri Jun 23 08:44:55 EDT 2023
distribution:         Red Hat Enterprise Linux Server 7.9 Maipo
number of CPUs:       24
** GPSS command failure for: ps h -o pid,ppid,user,comm -p 9401

error output:

** cannot detect shell: empty process stack
** GPSS command failure for: ps h -o pid,ppid,user,comm -p 9401

error output:

** cannot detect shell: empty process stack
apparent login shell: None
shell RC file:        NONE (does not exist)

--------------------- AFNI and related program tests ---------------------
which afni           : /software/afni/21.1.07/afni
afni version         : Precompiled binary linux_openmp_64: May 11 2021
                     : AFNI_21.1.07 'Domitian'
AFNI_version.txt     : AFNI_21.1.07, linux_openmp_64, May 11 2021
which python         : /usr/bin/python
python version       : 2.7.18
which R              : /software/r/4.1.1/b1/bin/R
R version            : R version 4.1.1 (2021-08-10) -- "Kick Things"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/gpfs/fs1/sfw2/afni/21.1.07/afni)
    R       : 1   (/gpfs/fs1/sfw2/r/4.1.1/b1/bin/R)
    python  : 1   (/usr/bin/python2.7)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 1   (/usr/bin/python3.6)


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 : success

R RHOME : /software/r/4.1.1/b1/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 : /software/miniconda/2.7.18/lib/python2.7/site-packages/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /software/hdf5/1.8.18/b1/bin:/software/gsl/2.5/b1/bin:/software/udunits2/2.2.20/usr/bin:/software/jdk/11.0.10/bin:/software/sqlite/3210000/bin:/software/proj/6.1.0/bin:/software/gdal/3.1.3/bin:/software/geos/3.7.2/bin:/software/gcc/9.1.0/libexec:/software/gcc/9.1.0/bin:/software/fftw3/3.3.10/b3/bin:/software/r/4.1.1/b1/bin:/software/libmng/2.0.3/b1/bin:/software/libpng/1.6.32/bin:/software/cuda/9.1/usr/local/cuda-9.1/bin:/software/fsl/6.0.5.1/bin:/software/slurm/current/bin:/software/firefox/current:/software/circ/bin:/xcatpost:/usr/bin:/bin:/sbin:/usr/sbin:/mnt/sysimage/bin:/mnt/sysimage/usr/bin:/mnt/sysimage/usr/sbin:/mnt/sysimage/sbin:/sbin:/usr/sbin:/xcatpost:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/software/afni/21.1.07/afni:/software/afni/21.1.07

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /software/hdf5/1.8.18/b1/lib:/software/mpfr/4.1.0/b1/lib:/software/gmp/6.2.1/b1/lib:/software/librsvg/2.40.20/usr/lib64:/software/gsl/2.5/b1/lib:/software/udunits2/2.2.20/usr/lib64:/software/jdk/11.0.10/lib:/software/sqlite/3210000/lib:/software/proj/6.1.0/lib:/software/gdal/3.1.3/lib:/software/miniconda/2.7.18/lib:/software/geos/3.7.2/lib:/software/gcc/9.1.0/lib64:/software/fftw3/3.3.10/b3/lib:/software/r/4.1.1/b1/lib64:/software/r/4.1.1/b1/lib64/R/lib:/software/libpng/1.2.50/usr/lib64:/software/libmng/2.0.3/b1/lib:/software/libpng/1.6.32/lib:/software/cuda/9.1/usr/local/cuda-9.1/lib64:/lib64:/software/slurm/current/lib64:/software/slurm/current/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 /software/afni/21.1.07

------------------------------ OS specific -------------------------------
which yum            : /usr/bin/yum
yum version          : There was a problem importing one of the Python modules


=========================  summary, please fix:  =========================
*  just be aware: login shell 'None', but our code examples use 'tcsh'
*  please run: cp /software/afni/21.1.07/AFNI.afnirc ~/.afnirc
*  please run: "suma -update_env" for .sumarc
*  please run: apsearch -update_all_afni_help
*  insufficient data for AFNI bootcamp

ptaylor · September 11, 2024, 11:02am

Cool. And noting this points in the system check's bottom section, "please fix":

... you could also run the following to have the default environment variable settings files for afni and suma (which you can tweak), respectively, as well as setting up the Tab-autocomplete of options for AFNI programs as you type (which I find extraordinarily helpful):

cp /software/afni/21.1.07/AFNI.afnirc ~/.afnirc
suma -update_env
apsearch -update_all_afni_help

If you are able to get an upgraded version of AFNI, using sswarper2 would probably be slightly more useful (see here). Because it is a tcsh script, you could even try just downloading it from our GitHub repo in some directory that is helpful:

# download sswarper2 script and make executable
curl -OL https://raw.githubusercontent.com/afni/afni/master/src/scripts_install/sswarper2
chmod 755 sswarper2

... and then use it like any other program:

# basic help example
    sswarper2                                    \
        -input  anat_t1w.nii.gz                  \
        -base   MNI152_2009_template_SSW.nii.gz  \
        -subid  sub-001                          \
        -odir   group/o.aw_sub-001

--pt