Thank you for the quick response. This unfortunately did not fix the problem. Below my output for afni_system_check.py. It seems I have two afni versions in my path. I wonder is that is causing the problem? Should I simply delete the file /usr/lib/afni/bin/afni?

mareike@mareike-linux:/usr/local/freesurfer$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.8.0-35-generic
version: #50-Ubuntu SMP Tue Dec 3 01:24:59 UTC 2013
distribution: Ubuntu 13.04 raring
number of CPUs: 4
apparent login shell: tcsh (current shell is bash)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/bin/afni
afni version : Precompiled binary =Debian-x86_64-1-gnu: Sep 9 2014
which python : /usr/bin/python
python version : 2.7.4
which R :
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 2
/usr/lib/afni/bin/afni_wrapper
/usr/lib/afni/bin/afni
R : 0
python : 1 (/usr/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 $HOME files...
.afnirc : missing
.sumarc : found
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4

------------------------------- path vars --------------------------------
PATH = /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/local/MATLAB/R2013a/bin/:/usr/lib/afni/bin

PYTHONPATH =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
atlas : found TT_N27+tlrc under /usr/share/afni/atlases

------------------------------ OS specific -------------------------------
have Ubuntu system: Ubuntu 13.04 raring

---------------------------- general comments ----------------------------
* consider only 1 version of AFNI in PATH
* consider copying AFNI.afnirc to ~/.afnirc
* consider running "apsearch -update_all_afni_help"