Yes, it's a dual boot system (Windows7 and Ubuntu 12.04 LTS)
I'm running FreeSurfer on Ubuntu.
Shared_Data is shared between Windows and Ubuntu.
I can try to install FreeSurfer on Linux /usr/local if you think that this can help.

Thanks!
Francesca


2014-05-14 17:09 GMT+03:00 dgw <dgwakeman@gmail.com>:
Francesca,

Is this a dual boot system (do you have multiple operating systems
installed on it)?

Are you running FreeSurfer in a virtual machine?

It sounds like another operating system may be controlling the
permissions of the /media/Shared_Data directory.

D

On Wed, May 14, 2014 at 9:51 AM, Francesca Strappini
<francescastrappini@gmail.com> wrote:
> 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.
>>
>
>
> _______________________________________________
> 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.
>
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