afni.nimh.nih.gov

Hi Rick,

Thank you very much for your help with this. I unfortunately ran into a likely unrelated error when attempting to run the below.

1d_tool.py -infile $AnimalID/$FolderID/dfile_VolReg2.1D -volreg2allineate -write $AnimalID/$FolderID/dfile_VolReg2_aff12.1D

I just tried to run '1d_tool.py' and get the same error:

>> 1d_tool.py
Traceback (most recent call last):
  File "/Users/ebaldelo/abin/1d_tool.py", line 2731, in <module>
    sys.exit(main())
  File "/Users/ebaldelo/abin/1d_tool.py", line 2719, in main
    aint = A1DInterface()
  File "/Users/ebaldelo/abin/1d_tool.py", line 1424, in __init__
    self.init_options()
  File "/Users/ebaldelo/abin/1d_tool.py", line 1756, in init_options
    acplist = LAD.g_1D_write_styles,
AttributeError: 'module' object has no attribute 'g_1D_write_styles'

I ran afni_system_check.py to check the status of things but don't see anything that sticks out to me (details below). Any thoughts or anything that sticks out to you?

>> afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              17.7.0
version:              Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution:         unknown Darwin
number of CPUs:       24
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/ebaldelo/abin/afni
afni version         : Precompiled binary macos_10.12_local: Jan  6 2023 
                     : AFNI_23.0.00 'Commodus'
AFNI_version.txt     : AFNI_23.0.00, macos_10.12_local, Jan 06 2023
which python         : /usr/bin/python
python version       : 2.7.10
which R              : /usr/local/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   (/Users/ebaldelo/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
    python  : 1   (/usr/bin/python)
    python2 : 0 
    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
    3dMVM                : FAILURE
        Error in dyn.load(ll) : 
          unable to load shared object '/Users/ebaldelo/abin/R_io.so':
          dlopen(/Users/ebaldelo/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
          Referenced from: /Users/ebaldelo/abin/R_io.so
          Reason: Incompatible library version: R_io.so requires version 3.6.0 or later, but libR.dylib provides version 3.5.0
        Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
        Execution halted

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

R RHOME : /Library/Frameworks/R.framework/Resources

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

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
   module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/ebaldelo/abin

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
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 /Users/ebaldelo/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.2

which brew           : /usr/local/bin/brew
brew version         : Homebrew 3.6.1

-- for PyQt4 under brew, consider running:
   brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
   -- found 'libXt' dylib files:
      /opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
   (so afni and suma may fail)

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  AFNI programs show FAILURE
*  please run: "suma -update_env" for .sumarc
*  insufficient data for AFNI bootcamp
*  OS X version might be old
*  consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace