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
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
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.
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
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!
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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!
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
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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
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.
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
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
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
-- 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
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
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.
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 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 > > > _______________________________________________ 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
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
-- 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
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
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
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 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 >> >> >> > _______________________________________________ > 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
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
-- 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
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
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
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.
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
freesurfer@nmr.mgh.harvard.edu
-
dgw -
Francesca Strappini -
Louis Nicholas Vinke -
Martin Reuter -
Z K