uber_subject.py

Hello,

I just installed afni on my laptop, and I’m having an error when I run uber_subject.py. Your help for resolving this issue would be much appreciated. I thought the command “brew install pyqt” lets me only install pyqt5 but not pyqt4, and maybe that’s why I’m having an error.

Thank you!

-Chuck

[jglabs-MacBook-Pro:~/afni] jglab% 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

[jglabs-MacBook-Pro:~/afni] jglab% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.3.0
version: Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64
distribution: 10.12.2 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/jglab/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Jan 3 2017
AFNI_version.txt : AFNI_17.0.00, macosx_10.7_Intel_64, Jan 03 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.3.2 (2016-10-31) – “Sincere Pumpkin Patch”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/jglab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 1 (/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4

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

PYTHONPATH = /usr/local/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 30 Dec 2016 [rickr]: applied updated FS reordering
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found FATCAT_DEMO under $HOME/AFNI_demos
top history: …CAT/FATCAT_DEMO.Distro, Wed Apr 8 12:41:00 EDT 2015
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/jglab/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.6

++ found valid link /usr/local/lib/libgomp.1.dylib
to /usr/local/Cellar/gcc/6.2.0/lib/gcc/6/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.50.2/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files, e.g. /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 comments ============================

  • have python3 but not python2
  • consider running: brew install pyqt
  • cannot tell if DYLD_LIBRARY_PATH includes /opt/X11/lib/flat_namespace

Hi-

This is a known-- and veeery new-- error. The Mac package manager, Homebrew, recently stopped including PyQt4 in their repository (they switched to PyQt5), so we have been trying to find the best solution but have not decided on it yet…

We might also note that uber_subject.py is a graphical interface for making an afni_proc.py command-- and actually, I think it is often easier to just go straight to making an afni_proc.py command than to wrangle with uber_subject (though, we will try to get this PyQt4 issue settled soon so that it will be back in use). There are several base examples in afni_proc.py’s help, which you could copy and then adjust to your processing needs. I believe Rick’s latest-and-greatest examples are #9-11b. Then for your group analysis, you can write a script to call the single afni_proc.py command for each subject, for example.

–pt