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:
- 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
- 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
- Does freeview open (just type 'freeview' after sourcing
FreeSurfer)?
shalim-ubunut:/media/Shared_Data/freesurfer> freeview /media/Shared_Data/freesurfer/bin/freeview: Permission