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 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
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-- 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
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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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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.