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
