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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icupsy
September 16, 2019 10:56AM
Hi experts,
I used the app to install the AFNI on Mac but the uber_subject does not work even after I used fink and brew to install the pyqt. Could you please help me on that? And I also install the python following the instructions but it did not show python2 in the output of checking file.

Thanks!


-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 8
apparent login shell: csh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/xc363/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 6 2019
: AFNI_19.2.23 'Claudius'
AFNI_version.txt : AFNI_19.2.23, macos_10.12_local, Sep 06 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/xc363/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/usr/bin/python
/sw/bin/python2.7
python2 : 0
python3 : 1 (/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

** have python3 but not python2

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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc

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

**************************************************
**************************************************


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

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)

-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/laps:/opt/X11/bin:/sw/bin:/Users/xc363/abin

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

R_LIBS =
LD_LIBRARY_PATH =
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) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: ...ay 2019 [rickr]: AFNI_pamenc updates to global_*.txt
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/xc363/aglobal

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.45.0
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.11

++ found 'brew' at /usr/local/bin/brew
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /usr/bin/python
++ 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 'csh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* check for partial install of PyQt4
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
* have brew? PyQt4, but non-brew python /usr/bin/python
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Subject Author Posted

uber_subject cannot work due to pyqt problem

icupsy September 16, 2019 10:56AM