Quick Start¶
Download Data¶
To download UK Biobank data for a subject, start by creating and initializing a new dataset. In this example, two data records with two instances (sessions) each are selected.
datalad create sub-1002532
cd sub-1002532
datalad ukb-init 1002532 20227_2_0 20227_3_0 20249_2_0 20249_3_0
After initialization, run ukb-update
to download data from the UK Biobank.
datalad ukb-update --keyfile <path_to_keyfile> --merge
This will create two branches:
incoming
: the pristine archives downloaded from UK Biobankincoming-native
: the extracted files in the original layout provided by the UK Biobank
With ukb-update --merge
, content is merged from incoming-native
into the active branch automatically.
Get Updates¶
To update a single subject’s dataset, simply re-run ukb-update
to
re-download the data and register any potential changes. Running ukb-update
will always re-download the data, regardless if there are upstream changes.
Again, the --merge
option will merge any updates into the active branch.
datalad ukb-update --keyfile <path_to_keyfile> --merge
Add or Remove Data Types¶
To add/remove data types, first re-initialize the dataset (with --force
) to
select the new data types. In this example, another data record with two
instances (sessions) is added to the list of selected data records.
datalad ukb-init --force 1002532 20227_2_0 20227_3_0 20249_2_0 20249_3_0 20250_2_0 20250_3_0
After re-initialization, run ukb-update
to download the data.
datalad ukb-update --keyfile <path_to_keyfile> --merge
Structure in BIDS¶
To enable a BIDS(-like) layout of the data, re-initialize the dataset with the
--bids
option. This option can also be used when first initializing the
dataset.
datalad ukb-init --force --bids 1002532 20227_2_0 20227_3_0 20249_2_0 20249_3_0 20250_2_0 20250_3_0
After re-initialization, run ukb-update
to create an additional
incoming-bids
branch containing a BIDS(-like) conversion of the extracted
downloads. If the --merge
option is specified, it will merge the
incoming-bids
branch into the active branch.
datalad ukb-update --keyfile <path_to_keyfile> --merge --force
The BIDS conversion only happens if the re-downloaded data is different from
the previously download data. If there are no changes to the content on
re-download, but you want to initiate the BIDS conversion, the --force
option can be used.
Save Space¶
The --drop
option can be used to avoid storing multiple copies of the same
data. In this example, the downloaded archives are kept and the extracted files
are dropped.
datalad ukb-update --keyfile <path_to_keyfile> --merge --force --drop extracted
It is also possible to keep the extracted content and drop the archives using
--drop archives
.