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
!chmod +x

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

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')

This notebook demonstrates how to use all Neurodesk applications in Google Colab:


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:

and more examples can be found here: