Hello Sir,

Output of afni_system_check.py -check_all is:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.5.0-54-generic
version: #81~precise1-Ubuntu SMP Tue Jul 15 04:02:22 UTC 2014
distribution: Ubuntu 12.04 precise
number of CPUs: 8
apparent login shell: bash

--------------------- AFNI and related program tests ---------------------
which afni : /home/bibl04/abin/afni
afni version : Precompiled binary linux_openmp_64: Oct 8 2014
which python : /usr/bin/python
python version : 2.7.3
which R : /usr/bin/R
R version : R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/bibl04/abin/afni)
R : 1 (/usr/bin/R)
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 : missing
.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/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/bibl04/abin

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 /home/bibl04/abin

------------------------------ OS specific -------------------------------
have Ubuntu system: Ubuntu 12.04 precise

---------------------------- general comments ----------------------------
* consider copying AFNI.afnirc to ~/.afnirc
* consider running "suma -update_env" for .sumarc
* consider running "apsearch -update_all_afni_help"

I think 3d SkullStrip shoild work now. Will you please let me know the command specifications and parameters in order to obtain a correct binary brain mask and skull stripped brain. I am using the volumes in nii format.