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