LWP-Wiki - User contributions [en]

FreeSurfer

2026-04-15T14:32:30Z

Chris:

[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki FreeSurfer] is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. 
 
To set up your environment run the command for the version you want to use:
. /opt/netapps/freesurfer/setup-freesurfer-v7.4.1.sh
. /opt/netapps/freesurfer/setup-freesurfer-v8.2.0.sh
. /opt/netapps/freesurfer/setup-freesurfer-dev.sh

To automatically set up your environment when you open a terminal, run the command for the version you want to use:
echo "source /opt/netapps/freesurfer/setup-freesurfer-v7.4.1" >> ~/.bashrc
echo "source /opt/netapps/freesurfer/setup-freesurfer-v8.2.0" >> ~/.bashrc
echo "source /opt/netapps/freesurfer/setup-freesurfer-dev" >> ~/.bashrc

To check if FreeSurfer is working, you can run the following command:
/opt/netapps/freesurfer/setup-freesurfer-v7.4.1.sh -t
/opt/netapps/freesurfer/setup-freesurfer-v8.2.0.sh -t
/opt/netapps/freesurfer/setup-freesurfer-dev.sh -t

FreeSurfer

2026-04-15T13:31:21Z

Chris:

[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki FreeSurfer] is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. 
 
To set up your environment run the command for the version you want to use:
. /opt/netapps/freesurfer/setup-freesurfer-v7.4.1.sh
. /opt/netapps/freesurfer/setup-freesurfer-v8.2.0.sh

To automatically set up your environment when you open a terminal, run the command for the version you want to use:
echo "source /opt/netapps/freesurfer/setup-freesurfer-v7.4.1" >> ~/.bashrc
echo "source /opt/netapps/freesurfer/setup-freesurfer-v8.2.0" >> ~/.bashrc

To check if FreeSurfer is working, you can run the following command:
/opt/netapps/freesurfer/setup-freesurfer-v7.4.1.sh -t
/opt/netapps/freesurfer/setup-freesurfer-v8.2.0.sh -t

Main Page

2026-04-15T09:26:59Z

Chris:

[[Category:Main]]
= LWP Wiki =
Welcome to the LWP-Wiki!! For general LWP information, [http://myuniversity.rug.nl/infonet/medewerkers/ict/werkplek/werkplekken/linuxwerkplek/ the LWP main page] is the starting point. 
If you're having trouble on your LWP, our [[FAQ]] is a good place to take a look first. We might already have solved your problem once or twice before. 


== Announcements ==
{{Announcement| [[User:Chris|Chris]] ([[User talk:Chris|talk]]) 15:42, 2 December 2025 (UTC)| New LWP version available, Ubuntu 24.04 LTS. [[Installing_the_LWP| Install instructions here]].}}
{{Announcement| [[User:Chris|Chris]] ([[User talk:Chris|talk]]) 09:26, 15 April 2026 (UTC)| '''[[FreeSurfer]]''' neuroimaging software and '''[[ITK-SNAP]]''' medical image segmentation tool have been made available. Click the links for setup instructions.}}
If you're having trouble with your LWP and the solution isn't in our [[FAQ]], contact us by using the '''support''' program on the LWP's (if possible) by entering "support" on a LWP command line or selecting it from the menu. 
For more general questions you can contact us by sending a mail to [mailto:lwp@rug.nl lwp@rug.nl].

FreeSurfer

2026-04-15T09:26:31Z

Chris: Created page with "[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki FreeSurfer] is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. To set up your environment run the command for the version you want to use: . /opt/netapps/freesurfer/setup-freesurfer-v7.4.1.sh . /opt/netapps/freesurfer/setup-freesurfer-v8.2.0.sh To automatically set up your environment when you open a te..."

ITK-SNAP

2026-04-15T09:20:02Z

Chris: Created page with "[https://www.itksnap.org/pmwiki/pmwiki.php?n=Main.HomePage ITK-SNAP] is a free, open-source, multi-platform software application used to segment structures in 3D and 4D biomedical images. To set up your environment run the following command: . /opt/netapps/itksnap/setup-itksnap.sh To automatically set up your environment when you open a terminal: echo "source /opt/netapps/itksnap/setup-itksnap.sh" >> ~/.bashrc"

[https://www.itksnap.org/pmwiki/pmwiki.php?n=Main.HomePage ITK-SNAP] is a free, open-source, multi-platform software application used to segment structures in 3D and 4D biomedical images. 
 
To set up your environment run the following command:
. /opt/netapps/itksnap/setup-itksnap.sh

To automatically set up your environment when you open a terminal: 
echo "source /opt/netapps/itksnap/setup-itksnap.sh" >> ~/.bashrc

Installing the LWP

2026-02-17T11:13:20Z

2024-06-12T11:49:45Z

Chris:

[[Category:home-directory-faq]]
==== TL;DR ====
You need to authenticate with your password at least once per week in order to keep access to your home directory.
To do this, run the <code>kinit</code> command explicitly or unlock your screen.

==== Details ====
Your home directory is secured using -what is called- kerberos tickets. As
long as you have such a ticket you have access to your home directory. When the
ticket is deleted, lost or expired you lose access to your home directory (and
project directory/directories)

You get such a ticket:
* automatically when you login with your password (as opposed to e.g. with SSH public key)
* automatically when you unlock your screen using your password
* when you explicitly enter the <code>kinit</code> command (it will prompt for your password)

These tickets expire after 12 hours. But the validity can be extended *without*
re-entering your password up to max 1 week.

When you login on an LWP, ticket validity is extended automatically to one week.

So, in order to have uninterrupted access to your home directory, you need to either:
* Run the <code>kinit</code> command every week (or every day or so if that's more convenient)
* Make sure you unlock your screen at least once a week, e.g. by configuring automatic screen locking.

Advanced commands:

;<code>klist</code>
: Shows kerberos ticket information
;<code>kadvice</code>
: Shows verbose kerberos ticket information, including advice on e.g. SSH command line option to use for maximum ticket validity.

If you use SSH from within the university network to access an LWP, it is
possible to authenticate without providing your password (e.g. by using public
key authentication or even a kerberos ticket). That is were it gets more
complicated. In those cases please run the <code>kadvice</code> script mentioned above to
get some advice on the optimal SSH command line options to use.

==== Keytab ====
A more permanent option is to create a keytab file. 
'''!NOTE''' Uppercase [PSFG] in username is required. 
'''!NOTE''' You are effectively storing the login credentials to an account in a file on the system, so handle with care! Don't use this on a shared system. 
Login on a LWP; In a terminal enter the following command to open the '''ktutil''' command interface:
$ ktutil
Give these commands to create a keytab file (replace P123456 with a valid username):
ktutil: add_entry -password -p P123456 -k 1 -e aes256-cts-hmac-sha1-96 -s WORKSPACE.RUG.NLP123456
# Input your password.
ktutil: write_kt /tmp/kt_P123456
ktutil: quit
Now use the following command to run your jobs with the credentials file you've just created:
$ k5start -Ubf /tmp/kt_P123456 <command you want to keep running>