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  

|
November 08, 2016 03:21PM
Dear AFNI experts,

I updated XQuartz today and now SUMA won't work. This is the error I get:

Error: attempt to add non-widget child "dsm" to parent "[A] SUMA" which supports only widgets.

This is the output of the system_check:

[isabellemacbook:~] Isa% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 14.5.0
version: Darwin Kernel Version 14.5.0: Sun Sep 25 22:07:15 PDT 2016; root:xnu-2782.50.9~1/RELEASE_X86_64
distribution: 10.10.5 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/Isa/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Nov 4 2016
AFNI_version.txt : AFNI_16.3.08, macosx_10.7_Intel_64, Nov 04 2016
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/bin/R
R version : R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/Isa/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R)
python : 2
/usr/bin/python
/Applications/anaconda/bin/python2.7

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 : FAILURE

oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!


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/fsl/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/Isa/abin:/Users/Isa/abin:/Applications/anaconda/bin:/Applications/scilpy/scripts:/Users/Isa/mrtrix2/bin:/Users/Isa/antsbin/bin:/Users/Isa/tract_querier/scripts:/Applications/anaconda/lib/python2.7/site-packages/

PYTHONPATH = /Applications/scilpy/

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH = /Users/Isa/abin


------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/Isa/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : 0.9.5

++ found PyQt4 under /usr/local/lib/python2.7/site-packages

============================ summary comments ============================
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH

Any idea what I can do to fix this issue?

Thank you!

Isabelle
Subject Author Posted

Suma error after update Xquarts

isades November 08, 2016 03:21PM

Re: Suma error after update Xquarts

Bob Cox November 08, 2016 03:58PM