Neurodesktop access

How to use Neurodesktop on the server
Author

NZ

Published

September 27, 2024

Neurodesktop is a Linux environment specifically developed for open and reproducible neuroimaging. For details, see https://www.neurodesk.org

To use the neurodesktop on our lab’s server, please follow the steps below.

Neurodesktop is accessible from the office, via VPN (for employees only, or for those who’s student account has been explicitly activated for server access by the IT), and in the student computer room.

General

  1. In your browser, type https://pslg-nv1.uni-graz.at and sign up for a account

  2. After you sign up, You account needs to be authorized by the technical staff. This may take a few days. If there is no progress, please check back with us. @Lab members: please use the same account name as your local server user account. That way you will automatically have access permissions for all your data via the serverpath /storage/neurodesk/users/{username}. For example, Natalia should use natalia_nv as username.

  3. Once your account is authorized, you can sing in with your credentials and you will see a JupyterLab session. You can start the neurodesktop by clicking on the icon. The session can be suspended and resumed later, with all your applications remaining as you left them.

    You should see the desktop with all the apps:


  4. Using FitLins (not a part of neurodesktop basic set of tools) with Singularity:


    singularity run /shared/poldracklab_fitlins_latest-2022-10-17-32670dc66bf7.simg [your fitlins commands]

  5. If you don’t have a local server account, you can transfer the data via nextcloud client, which is included in neurodsktop


    There are different Neurodesktop versions available on the JupyterHub. If you need another Jupyter Notebook or another version of the Neurodesk, please let us know. Additionally, if anything is not working as expected, do not hesitate to report it.

    Enjoy!

Lab members

Folder mappings: (left is server right is neurodesk)


/storage -> /storage
/storage/neurodesk/shared -> /shared
/storage/neurodesk/users/{username} -> /home/jovyan

Only these three folders are persistent.

Using FreeSurfer/View with /storage Data

To force freesurfer/freeview to see the /storage folder, source freesurfer from the terminal as follows

ml freesurfer/7.4.1
cd /storage
freeview