On 31 Oct 2014, at 16:35, zkaufman@nmr.mgh.harvard.edu wrote:

Yes, please try running as root and get back when you have the chance.
This is a very odd issue and your results when running as root will
provide insight.

-Zeke

Hi Z K,

Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
installed with the latest freesurfer version did not work while others
finished the processing in a reasonable processing time and I got the
results.

Also, I have a PC at my office installed with the latest freesurfer
version
and it works fine. So I have two PCs installed with the latest Freesurfer
(one of them which does not work is in the lab).


To summarize:
All PCs (16 PCs in the lab and 1 in my office) are installed with latest
Ubuntu version 14.04 64 bits
15 PCs in the lab are installed with freesurfer 5.0.0 version
1 PC in the lab is installed with the latest freesurfer version (does not
work, permission denied)
1 PC in my office is installed with the latest freesurfer version (works
fine)

All these PCs have Ubuntu 14.04 64bit installed on them.



No, I am not using any vitual machine.

Regarding the root user, I will try it on Sunday as I am away for a couple
of days.

Many thanks for your continuous support.

Ali




On Thu, Oct 30, 2014 at 6:34 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Ali,

First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
working properly? I am under the impression that versions of freesurfer
pre-version 5.3 will not work on newer linux distributions?


In regards to your current permision denied issue... What happens if you
try and run tkmedit as root user? Also, you not using virtual machine
setup are you?

-Zeke

On 10/30/2014 06:27 AM, Ali Radaideh wrote:

It does not work. This is really strange

On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu>> wrote:

   I beleive it should have a lower case X, as in:

   chmod -R a+x freesurfer/bin

   -Zeke

   On 10/28/2014 01:19 AM, Ali Radaideh wrote:

Dear Douglas

Thanks for your reply. unfortunatey I still get the same error.

   Here is

the terminal output. Is there anything else I can do?

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

--------

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~> tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~>


On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

   <mailto:greve@nmr.mgh.harvard.edu
   <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

   Try chmod -R a+X freesurfer/bin


   On 10/26/14 1:57 PM, Ali Radaideh wrote:

   Dear FreeSurfer users,

   I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One

   of the

   PCs has the latest version of freesurfer 5.3.0 while the

others

   have the version 5.0.0. The PC that is installed with the

latest

   version freesurfer 5.3.0 does not allow me to run any

   command and

   everytime I try a command such such as tkmedit i get the

   following

   error
   /usr/local/freesurfer/bin/tkmedit: permission denied.

   I have tried to change the permission settings
   sudo chown -R imaging:imaging freesurfer

   but did not work.

   Any ideas why is this happening although I have done the

same

   thing to other PCs and they are working fine.

   â€‹Thanks in advance,
   Ali​

   --
   /Ali M. Al-Radaideh. PhD
   Assistant Professor
   Head of Department of Medical Imaging
   Vice Dean of the Faculty of Allied Health Sciences
   The Hashemite University,
   Zarqa, Jordan
   W.phone +962 5 3903333 ext.5422, 5355, 5364
   Email: ali.radaideh@hu.edu.jo

   <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo
   <mailto:ali.radaideh@hu.edu.jo>>

   /
   /webpage:

http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/

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--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>

   <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>>

/
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--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>
/
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--








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email:
ali.radaideh@hu.edu.jo <ali.radaideh@hu.edu.jo>*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
<http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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