This software is a DataLad extension that equips DataLad with a set of commands to obtain, monitor, and restructure imaging data releases of the UK Biobank. It is designed to download MRI bulk data, track additions/redactions/fixes from the UK Biobank, and (optionally) restructure into BIDS layout.
What is the UK Biobank?¶
The UK Biobank is a national and international health resource with unparalleled research opportunities, open to all bona fide health researchers. The UK Biobank aims to improve the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses — including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression, and forms of dementia. It is following the health and well-being of 500,000 volunteer participants, and aims to collect imaging data for 100,000 of the participants. It provides health information, which does not identify participants, to approved researchers in the UK and overseas, from academia and industry.
In order to download data from the UK Biobank with
will need the following:
- Approved access to download the UK Biobank data. This can be gained as the Principal Investigator (PI) on an approved application, or as a collaborator with “delegate” status.
- A keyfile (file containing a 64-character password that is provided by the UK Biobank after a successful application)
- A bulk data file (requires the download of the main dataset and conversion to a bulk file; see the UK Biobank accessing data guide)
- The ukbfetch commandline tool
The easiest way to install the latest version of
datalad-ukbiobank is from
PyPi. It is recommended to use a dedicated virtual environment:
# create and enter a new virtual environment (optional) python3 -m venv ~/.venvs/datalad source ~/.venvs/datalad/bin/activate # install from PyPi pip install datalad_ukbiobank