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OpenNeuro command line interface

This tool allows you to upload and download OpenNeuro.org datasets without a browser.

Install

  1. Install Node.js (version 10 or higher)
  2. In a terminal type: npm install -g openneuro-cli

If you are using yarn you can also perform the installation with yarn global add openneuro-cli (make sure the installation folder is part of your PATH by adding export PATH="$(yarn global bin):$PATH" to ~/.bashrc)

Setup

The setup step is needed for both uploading and downloading data from OpenNeuro.

Run openneuro login to configure credentials. This prompts you for the required configuration fields and saves this to .openneuro in your home directory or profile. openneuro login will require you to enter an API key. You can obtain an API key via a browser at https://openneuro.org/keygen after logging to the OpenNeuro platform via one of the provided authentification services (for example ORCID).

After successfully running openneuro login, you can manually configure custom servers by editing the .openneuro file.

Usage

Uploading datasets

To upload a new dataset:

openneuro upload <dataset directory>

Your dataset must pass validation to upload but warnings can be skipped with openneuro upload -i <dataset directory>. A default label is set using the directory name.

To resume an interrupted upload or add files to an existing dataset:

openneuro upload --dataset <accession number> <dataset directory>

where <accession_number> is a unique dataset identifier that can be found in the URL. For example accession number for https://openneuro.org/datasets/ds001555 is ds001555.

This command will add or replace any files in the dataset but does not delete any files that are only present in the server copy of the dataset.

Downloading datasets

To download a snapshot:

openneuro download <accession number> <destination directory>

To download the current draft files:

openneuro download --draft <accession number> <destination directory>

If the destination directory does not exist, it will be created. Any files from the dataset that are already present in the directory will be skipped, allowing you to resume an interrupted download.

Errors

Package: OpenNeuro CLI download option

Issue: TypeError: path must be a string or Buffer

Solution: This error is due to a failure to read the ~/.openneuro configuration file. This file can be created with the command openneuro login, see the "Setup" step above.