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

History of AFNI updates  

|
July 29, 2020 06:33PM
Hi,

I am new to AFNI. I installed AFNI in MacOS Catalina 10.15.6. I am trying to use the uber_subject.py command. However, I keep getting the error:

uber_subject.py

**** failed to import PyQt4.QtGui ****

PyQt4 must be installed to run the uber_subject.py GUI
--> see the output of: uber_subject.py -help_install

When I follow the help, I get the following:
brew install pyqt
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> Updated Formulae
Updated 3 formulae.

Warning: pyqt 5.15.0 is already installed and up-to-date
To reinstall 5.15.0, run `brew reinstall pyqt`

MY Python path is also set to :
echo $PYTHONPATH: /usr/local/lib/python3.8/site-packages


Following is result of afni_system_check

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/matava/abin/afni
afni version : Precompiled binary macos_10.12_local: Jul 23 2020
: AFNI_20.2.06 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.06, macos_10.12_local, Jul 23 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/matava/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/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 : /Library/Frameworks/R.framework/Resources

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

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

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

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/matava/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.9

-- 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'
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace


Can anyone help me out here?
Subject Author Posted

unable to run uber_subject.py

avantika July 29, 2020 06:33PM

Re: unable to run uber_subject.py

ptaylor July 30, 2020 09:38AM

Re: unable to run uber_subject.py

mrinmayik August 24, 2021 10:44PM

Re: unable to run uber_subject.py

ptaylor August 25, 2021 03:34PM

Re: unable to run uber_subject.py

mrinmayik August 25, 2021 05:50PM

Re: unable to run uber_subject.py

ptaylor August 25, 2021 06:26PM