Not exactly sure why your getting a permission denied error. Can you please try the following and provide us with the relevant output?
1) What is the output of the following: ls -ld $FREESURFER_HOME/bin
2) After sourcing FreeSurfer, what happens when you type: tkmedit -f $SUBJECTS_DIR/sample-001.mgz
3) Does freeview open (just type 'freeview' after sourcing FreeSurfer)?
-Zeke
On 05/13/2014 06:51 AM, Francesca Strappini wrote:
Sure, thanks!
tcsh shalim-ubunut:/media/Shared_Data/freesurfer> setenv FREESURFER_HOME /media/Shared_Data/freesurfer shalim-ubunut:/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
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!
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