3dAllineate: FAILURE

I’m having some trouble with 3dAllineate when trying to run proc.FT created with uber_subject.py.

afni_system_check.py shows:

3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/Shared/abin/3dAllineate
Reason: image not found

How do I fix 3dAllineate? Not sure why it isn’t working when it is in the same directory as the rest of the AFNI programs.



What are the outputs of:

$ afni -ver

$ afni_system_check.py -check_all



(And I’ll assume that you went through the AFNI install instructions for your system here:


If you’re doing this on a Mac, then you need to update the symbolic link to the newer version than the one in the instructions.

ln -s /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/libgomp.1.dylib /usr/local/lib/libgomp.1.dylib

So instead of 5.2.0 and gcc/5, replace the path the libgomp.1.dylib with the path to where it actually is. Find the path to that file with :

find /usr/local/Cellar/gcc -name libgomp.1.dylib

I did not install AFNI on this mac, I inherited this mac from another person and AFNI was already installed.

Output of afni -ver is:

Precompiled binary macosx_10.7_Intel_64: Dec 10 2014 (Version AFNI_2011_12_21_1014)

Output of afni_system_check.py -check_all is:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.4.0
version: Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64
distribution: 10.11.4 x86_64
number of CPUs: 4
apparent login shell: tcsh

--------------------- AFNI and related program tests ---------------------
which afni : /Users/Shared/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Dec 10 2014
which python : /usr/bin/python
python version : 2.7.10
which R :
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/Shared/abin/afni)
R : 0
python : 1 (/usr/bin/python)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/Shared/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : success

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

------------------------------ python libs -------------------------------

** python module not found: PyQt4

 -> please see the output of "uber_subject.py -help_install"

------------------------------- path vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/Shared/abin:/Users/Nick/bin:.


------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME/work/PSYC571
top history: 16 Oct 2015 [rickr]: added FT_analysis/PPI directory, with PPI scripts
data dir : missing suma_demo
atlas : found TT_N27+tlrc under /Users/Shared/abin

------------------------------ OS specific -------------------------------
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
(consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH)

---------------------------- general comments ----------------------------

  • consider copying AFNI.afnirc to ~/.afnirc
  • consider running “suma -update_env” for .sumarc

Thank you, this seems to have worked!