Hi Paul,

Hope you're well!

I need uber_subject.py for an "introduction to fMRI preprocessing workshop" I'm conducting, and thought a GUI would be useful to demonstrate how the "theory of preprocessing" they learned would translate to actually processing the data.

I'm having similar issues with starting uber_subject.py. I tried running uber_subject.py from both tcsh and bash and get the same "failed to import PyQt4.QtGui". However, I am able to start afni and suma.

My $PATH is /usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/anaconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/mrinmayi/abin:/Users/mrinmayi/abin.
And $PYTHONPATH is /usr/local/lib/python2.7/site-packages

Homebrew says "pyqt 6.1.1 is already installed and up-to-date". And my afni_system_check.py -check_all generates the following:


-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 20.6.0
version: Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:31 PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64
distribution: 10.16
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/mrinmayi/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 22 2021
: AFNI_21.2.05 'Nerva'
AFNI_version.txt : AFNI_21.2.05, macos_10.12_local, Aug 22 2021
which python : /opt/local/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/mrinmayi/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/3.6/bin/python3.6
/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 : FAILURE

oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: metafor!


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/3.6/bin/python3.6)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/anaconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/mrinmayi/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 : found AFNI_data6 under $HOME/AFNI_Bootcamp
top history: ...7 Oct 2018 [rickr]: re-add FT_white.nii, FT_vent.nii
data dir : found AFNI_demos under $HOME/AFNI_Bootcamp
top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME/AFNI_Bootcamp
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME/AFNI_Bootcamp
atlas : found TT_N27+tlrc under /Users/mrinmayi/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.0_beta3

which brew : /usr/local/bin/brew
brew version : Homebrew 3.2.9
which port : /opt/local/bin/port
port version : Error: Current platform "darwin 20" does not match expected platform "darwin 19"

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.68.3/lib/libglib-2.0.dylib
++ 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 'bash'...
++ 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 'bash', but our code examples use 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* missing R packages (see rPkgsInstall)


Is there something else I'm missing?

Thank you,
Mrinmayi

PS: Even if I do get uber_subject working, I'll be sure to tell the attendees that afni_proc is the preferred way to do preprocessing, and show them how to use it as well!