AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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MayaSa
July 12, 2022 06:06AM
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
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Subject Author Posted

QC file for proc.py with tedana

MayaSa July 10, 2022 02:53AM

Re: QC file for proc.py with tedana

ptaylor July 10, 2022 06:53PM

Re: QC file for proc.py with tedana

MayaSa July 12, 2022 06:06AM

Re: QC file for proc.py with tedana

ptaylor July 12, 2022 08:30AM

Re: QC file for proc.py with tedana

ptaylor July 13, 2022 09:23AM