datalad ukb-init

Synopsis

datalad ukb-init [-h] [-f] [--bids] [-d DATASET] PARTICPANT-ID DATARECORD-ID [DATARECORD-ID ...]

Description

Initialize an existing dataset to track a UKBiobank participant

A batch file for the ‘ukbfetch’ tool will be generated and placed into the dataset. By selecting the relevant data records, raw and/or preprocessed data will be tracked.

After initialization the dataset will contain at least three branches:

  • ‘incoming’: to track the pristine ZIP files downloaded from UKB
  • ‘incoming-native’: to track individual files (some extracted from ZIP files)
  • ‘incoming-bids’: to track individual files in a layout where file name conform to BIDS-conventions
  • main branch: based off of incoming-native or incoming-bids (if enabled) with potential manual modifications applied

Examples

Initialize a dataset in the current directory:

% datalad ukb-init 5874415 20227_2_0 20249_2_0

Initialize a dataset in the current directory in BIDS layout:

% datalad ukb-init --bids 5874415 20227_2_0

Options

PARTICPANT-ID

UKBiobank participant ID to use for this dataset (note: these encoded IDs are unique to each application/project). Constraints: value must be a string

DATARECORD-ID

One or more data record identifiers. Constraints: value must be a string

-h, --help, --help-np

show this help message. –help-np forcefully disables the use of a pager for displaying the help message

-f, --force

force (re-)initialization.

--bids

additionally maintain an incoming-bids branch with a BIDS-like organization.

-d DATASET, --dataset DATASET

specify the dataset to perform the initialization on. Constraints: Value must be a Dataset or a valid identifier of a Dataset (e.g. a path)

Authors

datalad is developed by Michael Hanke <michael.hanke@gmail.com>.