I am having the same problem. I ran the test command and got this. It does look like there are some problems... but I don't know how to fix.
kefka:/Volumes/lt-tib/mbsr-working/scripts$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 14.5.0
version: Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64
distribution: 10.10.5 x86_64
number of CPUs: 4
apparent login shell: bash
--------------------- AFNI and related program tests ---------------------
which afni : /apps/x86_64_darwin14/AFNI_latest/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Aug 12 2015
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 (/apps/AFNI_2011_12_21_1014_2015Aug19/macosx_10.7_Intel_64/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R)
python : 2
/home/perlman/bin/python
/usr/bin/python
testing ability to start various programs...
afni : success
suma : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /apps/x86_64_darwin14/AFNI_latest/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /apps/x86_64_darwin14/AFNI_latest/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /apps/x86_64_darwin14/AFNI_latest/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /apps/x86_64_darwin14/AFNI_latest/SurfMesh
Reason: image not found
checking for $HOME files...
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
---------------------------------------------------------
** python module not found: PyQt4
-> please see the output of "uber_subject.py -help_install"
------------------------------- path vars --------------------------------
PATH = ~/bin:/opt/local/bin:/sw/bin:/home/perlman/bin:/apps/x86_64_darwin14/matlab-latest/bin:/apps/x86_64_darwin14/AFNI_latest:/apps/x86_64_darwin14/fsl-latest/bin:/apps/x86_64_darwin14/freesurfer-latest/bin:/apps/x86_64_darwin14/freesurfer-latest/fsfast/bin:/apps/x86_64_darwin14/freesurfer-latest/tktools:/apps/x86_64_darwin14/freesurfer-latest/mni/bin:/apps/ruby/x86_64_darwin14/bin:/apps/x86_64_darwin14/camino-latest/bin:/usr/local/Python/Versions/2.6.5/bin:/apps/noarch/current/bin:/apps/x86_64_darwin14/current/bin:/bin:/usr/bin:/sbin:/usr/sbin:/apps/vack-tools/bin
PYTHONPATH = /home/perlman/bin/python:/apps/noarch/current/lib:/apps/x86_64_darwin14/current/lib:/apps/python/python_apps/tro
LD_LIBRARY_PATH = :/usr/bin/
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
atlas : found TT_N27+tlrc under /apps/x86_64_darwin14/AFNI_latest
------------------------------ OS specific -------------------------------
---------------------------- general comments ----------------------------
* consider running "suma -update_env" for .sumarc
* consider running "apsearch -update_all_afni_help"
