Ok, thank you!

I sourced freesurfer and then I tried:
cd $FREESURFER_HOME
sudo chmod -R a+rX *

But I still get the same error:
shalim-ubunut:/media/Shared_Data/freesurfer> freeview
/media/Shared_Data/freesurfer/bin/freeview: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer> sudo freeview
sudo: freeview: command not found

Best
Francesca





2014-05-14 16:35 GMT+03:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu>:
Hi Francesca,

you need to make sure that the current user has read and execute permissions of the Freesurfer files. Either make sure that the FreeSurfer directory is in the same group as the user and give group rights, or give read and execute rights to everyone.

source freesurfer first

cd $FREESURFER_HOME
sudo chmod -R g+rX *
for setting group rights, assuming the group is the same, you can also change the group via:
sudo chgrp -R groupname *

where groupname is the new group.

If you want to give world read/execute permissions do this:
cd $FREESURFER_HOME
sudo chmod -R a+rX *


Best, Martin


On 05/14/2014 04:16 AM, Francesca Strappini wrote:
Hi, thanks for the help!
These are the outputs:

> 1) What is the output of the following:
> ls -ld $FREESURFER_HOME/bin

drwxrwxrwx 1 francesca francesca 118784 May 14  2013 /media/Shared_Data/freesurfer/bin

> 2) After sourcing FreeSurfer, what happens when you type:
> tkmedit -f $SUBJECTS_DIR/sample-001.mgz

shalim-ubunut:/media/Shared_Data/freesurfer>  tkmedit -f $SUBJECTS_DIR/sample-001.mgz
/media/Shared_Data/freesurfer/bin/tkmedit: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer> sudo  tkmedit -f $SUBJECTS_DIR/sample-001.mgz
[sudo] password for francesca:
sudo: tkmedit: command not found


> 3) Does freeview open (just type 'freeview' after sourcing FreeSurfer)?

shalim-ubunut:/media/Shared_Data/freesurfer> freeview
/media/Shared_Data/freesurfer/bin/freeview: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer> sudo freeview
sudo: freeview: command not found

Francesca









>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /media/Shared_Data/freesurfer
>> FSFAST_HOME       /media/Shared_Data/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR      /media/Shared_Data/freesurfer/subjects
>> MNI_DIR           /media/Shared_Data/freesurfer/mni
>>
>> shalim-ubunut:/media/Shared_Data/freesurfer> pwd
>> /media/Shared_Data/freesurfer
>>
>> shalim-ubunut:/media/Shared_Data/freesurfer> tkmedit bert orig.mgz
>> /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied.
>>
>> shalim-ubunut:/media/Shared_Data/freesurfer> sudo tkmedit bert orig.mgz
>> sudo: tkmedit: command not found
>>
>> shalim-ubunut:/media/Shared_Data/freesurfer/bin> ls -la tkmedit
>> -rwxrwxrwx 1 francesca francesca 102 May 14  2013 tkmedit
>>
>> 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu>:
>>> Ok, could you send the entire terminal output?
>>> Thanks.
>>> -Louis
>>>
>>> On Mon, 12 May 2014, Francesca Strappini wrote:
>>>
>>>> Thanks Louis!
>>>>
>>>> Yes, I did run tkmedit from the same terminal window I have sourced
>>>> freesurfer...
>>>>
>>>> Francesca
>>>>
>>>> 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu>:
>>>>> Hi Francesca,
>>>>> Are you trying to run the tkmedit command in the same terminal window you
>>>>> have sourced freesurfer?  You'll need to source freesurfer in any new
>>>>> terminal window you open before being able to run any freesurfer commands.
>>>>>
>>>>> It's possible to set it up so that freesurfer is sourced automatically
>>>>> when opening a new terminal or setting up an alias to make the process
>>>>> quicker.
>>>>> -Louis
>>>>>
>>>>> On Sat, 10 May 2014, Francesca Strappini wrote:
>>>>>
>>>>>> Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64
>>>>>> and I have Ubuntu 12.04 LTS. I have set up the licence file and
>>>>>> configured freesurfer:
>>>>>>
>>>>>> tcsh
>>>>>> setenv FREESURFER_HOME /media/Shared_Data/freesurfer
>>>>>> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>>>>>>
>>>>>> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
>>>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>>>> FREESURFER_HOME   /media/Shared_Data/freesurfer
>>>>>> FSFAST_HOME       /media/Shared_Data/freesurfer/fsfast
>>>>>> FSF_OUTPUT_FORMAT nii.gz
>>>>>> SUBJECTS_DIR      /media/Shared_Data/freesurfer/subjects
>>>>>> MNI_DIR           /media/Shared_Data/freesurfer/mni
>>>>>>
>>>>>> When I try to run any type of command, like tkmedit bert orig.mgz, I
>>>>>> get this error:
>>>>>>
>>>>>> command not found.
>>>>>>
>>>>>> Thanks for the help!
>>>>>>
>>>>>> Francesca
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to whom it is
>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>>>>> contains patient information, please contact the Partners Compliance HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>>>>> but does not contain patient information, please contact the sender and properly
>>>>> dispose of the e-mail.
>>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.