Hi,
Thanks for the answer.
this is the output of afni_system_check.py -check_all:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 21.3.0
version: Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_X86_64
distribution: 10.16
number of CPUs: 20
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/ramotlab/abin/afni
afni version : Precompiled binary macos_10.12_local: Jul 28 2021
: AFNI_21.2.04 'Nerva'
AFNI_version.txt : AFNI_21.2.04, macos_10.12_local, Jul 28 2021
which python : /usr/bin/python
python version : 2.7.18
which R :
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/ramotlab/abin/afni)
R : 0
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/pythonwrapper.app/Contents/MacOS/pythonwrapper)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/pythonwrapper.app/Contents/MacOS/pythonwrapper)
python3 : 1 (/usr/bin/python3)
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 : R: Command not found.
checking for $HOME files...
.afnirc : found
.sumarc : found
.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/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/ramotlab/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ 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/ramotlab/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.1
which brew : /usr/local/bin/brew
brew version : Homebrew >=2.5.0 (shallow or no git repository)
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'zsh'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* failure under initial "AFNI and related program tests"
* insufficient data for AFNI bootcamp
So if I want to apply MEICA (ICA and not only optimally combined), should I use m_tedana in the proc.py function combine_method?
Maya
