How to download a dataset from OpenNeuro

How to download a dataset from OpenNeuro#

OpenNeuro is a free and open platform hosting over 1000 public, BIDS compliant datasets, including MRI, PET, MEG, EEG and iEEG datasets. In this tutorial, we’ll work with the data from one subject of one dataset that Gaponsetva (2023) used to validate MEGq. This section explains how to download a dataset from OpenNeuro:

  1. Find the dataset: navigate to the OpenNeuro homepage (or follow the hyperlink) and search for the dataset using the Accession Number: ds003483.

  2. Download options: When you click "Download" you’ll be presented with several options:

    • Download with your browser

    • Download from S3

    • Download with Node.js

    • Download with DataLad

    • Download with a shell script.

Given the dataset’s size (21 participants, 24.48 GB), dowloading the full dataset may be unnecessary. To save time and storage, we’ll dowload only one subject’s folder using Datalad.

Getting started with DataLad#

DataLadis a free and open source data tool for management of large datasets. It can be used to download a single subject folder from a dataset.

  1. Ensure git-annex is properly installed on your environment: DataLad requires git-annex version 8.20200309 (or higher). Verify your installation and, if needed, update git-annex.

    git annex version

  1. Install datalad within your environment:

    pip install datalad

  1. Clone the dataset repository: It copies the entire dataset’s structure, but only lightweight metada (such as .json), the actual data files (.fif in this case) are not downloaded, even thought they “broken links” placeholders will be created. Be sure you are working in your desired directory (with cd), then run:

    datalad install https\://github.com/OpenNeuroDatasets/ds003483.git

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  1. Download only the sub-009 folder: use the get command to download only the data for subject 009.

        datalad get ds003483/sub-009/