ok, thank you!

Francesca

On Wednesday, May 14, 2014, dgw <dgwakeman@gmail.com> wrote:
It doesn't need to be in /usr/local (I'm not sure if the FreeSurfer
team has a preferred install location), but it is probably simpler
(read: there may be some complex way to get it to work on a shared
directory, but it would take a lot of digging to figure out how) to
install it on the pure linux partition.

HTH,
D

On Wed, May 14, 2014 at 10:18 AM, Francesca Strappini
<francescastrappini@gmail.com> wrote:
> 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