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 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 mailto: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 mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu
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