Neurodesk Overview
Video tutorial
Click here to watch a 2 minute tutorial video from OHBM 2021
Introduction
Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. At Neurodesk, we believe that reproducibility should be a fundamental principle underlying neuroscientific data analysis (1). Analysis pipelines for neuroimaging data typically rely on specific versions of packages and software, and are dependent on their native operating system. These dependencies mean that a working analysis pipeline may fail or produce different results on a new computer, or even on the same computer after a software update. Neurodesk provides a platform in which anyone, anywhere, using any computer can reproduce your original research findings given the original data and analysis code.
What is a container?
The Neurodesk environment allows users to build and use containers for analysing neuroimaging data. Containers can be compared to virtual machines, in that they allow users to create a virtual, isolated computing environment with an operating system separate to that of the host machine. However, containers differ from virtual machines in that they virtualise software rather than hardware. Practically, this means that container images require few system resources to install, start-up quickly, and are easily portable between computers.
We recomment watching this excellent short video from the Australian Research Data Commons (ARDC) on research applications of software containers. To read more about Docker containers, visit the Docker webpage
The Neurodesk ecosystem
The Neurodesk ecosystem includes a number of tools for containerised analysis of neuroimaging data. These include:
Neurodesktop
If you’re new to Neurodesk, we recommend you begin with Neurodesktop.
Neurodesktop is a compact Docker container with a browser-accessible virtual desktop that allows you develop and implement data analysis pipelines as though you’re on your own computer. The neurodesktop container has the basic tools required for the analysis of fMRI and EEG data pre-installed. To get started, see: Neurodesktop
Neurocommand
Neurocommand offers the option to install and manage multiple distinct containers for more advanced users who prefer a command-line interface. Neurocommand is the recommended interface for users seeking to use Neurodesk in high performance computing (HPC) environments.
To get started, see: Neurocommand
Transparent-singularity
The applications pre-installed in neurodesktop and neurocommand are accessible through transparent-singularity, which allows users to transparently use containerised software as through it were installed natively.
To find out more about this open-source project, see: transparent-singularity
Neurocontainers
The neurocontainers repository contains build scripts for sub-containers which are wrapped around executables for neuroimaging data-analysis software. These neurocontainers can be used in combination with neurocommand or transparent-singularity.
To get started, see: Neurocontainers
Neurodocker
Neurodocker is a command-line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers.
To find out more about this open-source project, see: Neurodocker
References
- National Academies of Sciences, Engineering, and Medicine. 2019. Reproducibility and Replicability in Science. Washington, DC: The National Academies Press. https://doi.org/10.17226/25303.