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  

|
September 04, 2019 05:18AM
Hi experts,

I've used afni on MAC (high sierra 10.13.6) without any problem except for a function "@SUMA_Make_Spec_FS".
So I searched a similar case that I've gone through and I updated afni with this command:
@update.afni.binaries -defaults -package macos_10.12_local
But it required the latest XQuartz, so I updated XQuartz as 2.7.11. Updating afni was done (it said 'no update needed' at the end of processing) after updating XQuartz, but now I can't open the afni GUI window when I enter 'afni' or 'afni&' on a terminal.

I got these messages when I entered afni:
#################
Precompiled binary macos_10.12_local: Aug 29 2019 (Version AFNI_19.2.21 'Claudius')


** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to H Garavan for useful feedback

Initializing: X11++ AFNI is detached from terminal.
#################


And I get these messages when I entered 'afni_system_check.py -check_all':
################
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/minsunpark/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 29 2019
: AFNI_19.2.21 'Claudius'
AFNI_version.txt : AFNI_19.2.21, macos_10.12_local, Aug 29 2019
which python : /usr/local/bin/python
python version : 2.7.14
which R : /usr/local/bin/R
R version : R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/minsunpark/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/Library/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
3dClustSim : success
3dMVM : success

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

oo Warning:
These packages are not installed on the computer: brms!
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 -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

** 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)
/sw/bin/python2.7

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/fsl/bin:/Users/minsunpark/abin:/usr/local/fsl/bin:/Users/minsunpark/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ 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/minsunpark/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.8.5

++ found PyQt4 under /usr/local/lib/python2.7/site-packages
++ found valid link /usr/local/lib/libgomp.1.dylib
to /usr/local/Cellar/gcc/5.3.0/lib/gcc/5/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.46.2/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
++ yay, env var DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
###################


Plus, I saw a message like adding this 'DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace' to startup file.

I'd appreciate if you give any suggestions I can do!!!
Thank you very much!
Subject Author Posted

Erros after updating afni and XQuartz on Mac high sierra

Mpark September 04, 2019 05:18AM

Re: Erros after updating afni and XQuartz on Mac high sierra

Mpark September 04, 2019 05:42AM

Re: Erros after updating afni and XQuartz on Mac high sierra

rick reynolds September 04, 2019 09:20AM

Re: Erros after updating afni and XQuartz on Mac high sierra

Mpark September 05, 2019 12:27AM

Re: [SOLVED] Erros after updating afni and XQuartz on Mac high sierra

Mpark September 05, 2019 03:46AM

Re: [SOLVED] Erros after updating afni and XQuartz on Mac high sierra

rick reynolds September 05, 2019 08:47AM

Re: [SOLVED] Erros after updating afni and XQuartz on Mac high sierra

rick reynolds November 21, 2019 09:02AM