Google Colab
Neurodesk Singularity Containers for 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 here: https://github.com/NeuroDesk/example-notebooks/