couldn't get 3dALIGN script to work

I got FAILURE in 3dAllineate and 3dClustSim. And there’s also some suggestion to fix some IO errors. Please help!
Could it be from the XQuartz? I followed all the pre-processing steps on the AFNI website, but there was a little glitch in installing XQuartz. I entered those two lines of codes and nothing happened.
"touch ~/.cshrc
echo ‘setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace’ >> ~/.cshrc

touch ~/.bashrc
echo ‘export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace’ >> ~/.bashrc"

Below is the check for the system.
------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.6.0
version: Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64
distribution: 10.11.6 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/Apple/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Nov 9 2017
: AFNI_17.3.03
AFNI_version.txt : AFNI_17.3.03, macosx_10.7_Intel_64, Nov 09 2017
which python : /sw/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/Apple/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 2
python2 : 0
python3 : 0

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

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /sw/lib/qt4-mac/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

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

-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin:/Users/Apple/abin:/Users/Apple/abin:/Users/Apple/abin

PYTHONPATH = /sw/lib/qt4-mac/lib/python2.7/site-packages

DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: …PPI scripts are now based on FT_analysis/s05.ap.uber
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/Apple/abin

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.42.0

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

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .profile
  • AFNI programs show FAILURE


Rick has updated a lot of stuff in the Mac build realm, niceifying a lot of how the dependencies work for Mac, and there is now a new Mac tarball we recommend everyone using, called “macosx_10.7_local” (local because the local build on our end takes care of several dependencies, so you shouldn’t have to deal with the errors you are currently seeing). The instructions for downloading/installing are here:

So, you might just want to push your present AFNI binary directory to a new location:

cd /Users/Apple/
mv abin abin_OLD

… and then go through the AFNI download+install steps in the link above:

curl -O
tcsh @update.afni.binaries -defaults

Once you have run the system check again on the new install and verified that everything is awesome, you can probably just remove the abin_OLD (if you want, to free up space).


Thanks! But it didn’t change anything after I ran the code you suggested… I already installed “macosx_10.7_local” and walked through the instruction on that website before.
Could it be other problems?

Would you please show the same output
then, corresponding to the _local package? Those dyld errors
should not be present.

  • rick