helping running


I have been having issues getting to work on my laptop (MacOSMojave, version 10.14.5). I would appreciate any insight on how to fix this issue. I do have to admit that I am VERY new to using AFNI and it can simply be an error on my part but I just can figure out what the error is.

When I initial run I get this initial error:

PyQt4 must be installed to run the GUI
→ see the output of: -help_install

When running -check_all this is the output:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
distribution: 10.14.5 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/hectorarciniega/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 13 2019
: AFNI_19.2.24 ‘Claudius’
AFNI_version.txt : AFNI_19.2.24, macos_10.12_local, Sep 13 2019
which python : /usr/local/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) – “Great Truth”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/hectorarciniega/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
python2 : 1 (/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : 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: corrplot!
    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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/init.pyc

** have PyQt4, but cannot load QtCore, QtGui; error is:

Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named sip

** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/hectorarciniega/abin:/Applications/abin:/usr/bin:/Users/hectorarciniega/bin:/usr/local/lib

PYTHONPATH = /sw/bin/local/lib/python2.7/site-packages

DYLD_LIBRARY_PATH (sub-shell) = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = /Applications/abin

------------------------------ 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/hectorarciniega/abin

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

which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.13

++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** consider linking /usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.62.0_1/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • missing R packages (see rPkgsInstall)
  • check for partial install of PyQt4
  • insufficient data for AFNI bootcamp
  • consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH


Did you try installing PyQt4? The error message that you are getting points you to the help section on installing PyQt4 on different systems, as it said above:

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

In those help instructions, it has you set PYTHONPATH to a particular location, namely ‘/usr/local/lib/python2.7/site-packages’, and from your it doesn’t look like it is set correctly (it is set to a different location, on in your /sw/ tree, which I guess means one installed with fink).

It looks like your terminal is tcsh, so if you copy+paste the following:

echo "" >> ~/.cshrc
echo "setenv PYTHONPATH /usr/local/lib/python2.7/site-packages" >> ~/.cshrc 
echo "" >> ~/.cshrc
source ~/.cshrc

… can you open then?



I have installed PyQt4 using brew as mentioned in the -help_install. I did this before posting here. I have also followed your instructions in adding those paths onto my .cshrc but I am still unsuccessful in opening I am open to any other recommendations.


Hi HA,

I am a little confused by this, but at least your PYTHONPATH variable seems to be set to a fink tree, rather than a homebrew one.

It should probably be: /usr/local/lib/python2.7/site-packages
rather than: /sw/bin/local/lib/python2.7/site-packages

However, this will probably not matter, since the PyQt4 error is indeed coming from /usr/local.

We will try to get a homebrew machine set up and see what we find.

  • rick