Hosted

• 1: Bunya
• 2: Nectar Virtual Desktop Service
• 3: Play
• 4: Google Colab

1 - Bunya

Neurodesk is installed at the University of Queensland’s supercomputer “Bunya”. To access neurodesk tools you need to be in an interactive job (so either start a virtual desktop via Open On-Demand: https://bunya-ondemand.rcc.uq.edu.au/pun/sys/dashboard) or run:

salloc --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --mem=5G --job-name=TinyInteractive --time=01:00:00 --partition=debug --account=REPLACE_THIS_WITH_YOUR_AccountString srun --export=PATH,TERM,HOME,LANG --pty /bin/bash -l

Then load the neurodesk modules:

module use /sw/local/rocky8/noarch/neuro/software/neurocommand/local/containers/modules/
export APPTAINER_BINDPATH=/scratch,/QRISdata

Now you can list all modules (Neurodesk modules are the first ones in the list):

ml av

Or you can module load any tool you need:

ml qsmxt/6.4.1

If you want to use GUI applications (fsleyes, afni, suma, …) you need to overwrite the temporary directory to be /tmp (otherwise you get an error that it cannot connect to the DISPLAY):

export TMPDIR=/tmp 

NOTE: MRIQC has its $HOME variable hardcoded to be /home/mriqc. This leads to problems on Bunya. A workaround is to run this before mriqc:

export neurodesk_singularity_opts="--home $HOME:/home"

If you are missing an application, please contact mail.neurodesk@gmail.com and ask for the neurodesk installation to be updated on Bunya :)

2 - Nectar Virtual Desktop Service

There are a few differences between the open-source version of Neurodesk and what’s hosted on Nectar VDI:

1. There is no /neurodesktop-storage folder (the folder on the Desktop does not lead anywhere).
2. Files uploaded via drag and drop do not get stored on the desktop but in /home/vdiuser/thinclient_drives/GUACFS

Instructions for use

1. Go to https://desktop.rc.nectar.org.au/

2. Click on “Sign in”.

3. Choose the AAF option.

4. Choose your institution from the list.

5. Provide your email address and password.

6. Click on create a Workspace (you only need to do this when you sign in for the first time).

7. Fill form ‘Apply for new Workspace’ and submit.

8. Click on “EXPLORE”.

9. Click “VIEW DETAILS” under Neurodesktop:

10. Click “CREATE DESKTOP +” button on the top right corner.

11. Choose the desired availability zone.

12. Wait until everything is completed:

13. Click “OPEN DESKTOP ->”:

14. For a general guide on using the ARDC virtual desktops, click here: https://tutorials.rc.nectar.org.au/virtual-desktop-service/01-overview

15. For a specific explanation on how to launch the various applications available in the Neurodesktop desktop, follow the instructions here: https://www.neurodesk.org/docs/getting-started/neurodesktop/

3 - Play

4 - Google Colab

Open a notebook in Google Colab and run the following commands to set up the Neurodesk environment:

import os
os.environ["LD_PRELOAD"] = "";
os.environ["APPTAINER_BINDPATH"] = "/content"
os.environ["MPLCONFIGDIR"] = "/content/matplotlib-mpldir"
os.environ["LMOD_CMD"] = "/usr/share/lmod/lmod/libexec/lmod"

!curl -J -O https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/googlecolab_setup.sh
!chmod +x googlecolab_setup.sh
!./googlecolab_setup.sh

os.environ["MODULEPATH"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))

Once this setup is completed you can list the available Neurodesk applications like this:

import lmod
await lmod.avail()

and use applications like this:

await lmod.load('fsl/6.0.4')
!bet

This notebook demonstrates how to use all Neurodesk applications in Google Colab: https://colab.research.google.com/drive/1g5cnZxj1llRaHmOs4xSglqsXnFkQYuol?usp=sharing

This is a google colab notebook that shows how to integrate with google drive and contains an example how to run fMRIprep in google colab: https://colab.research.google.com/drive/11wVBkjNvrzo2TkUAILtWnPumAeFAfqkl?usp=sharing

and more examples can be found in our example library