Using the brainsets CLI

The brainsets CLI provides access to existing datasets, supported by the brainsets package.

Configuring data directories

First, configure the directories where brainsets will store raw and processed data:

brainsets config set

You will be prompted to enter the paths to the raw and processed data directories:

$> brainsets config set
Enter raw data directory: ./data/raw
Enter processed data directory: ./data/processed

You can update the configuration at any time by running the config set command again.

To view the current configuration:

brainsets config show

Listing available datasets

You can list the available datasets by running the list command:

brainsets list

Preparing data

You can prepare a dataset by running the prepare command:

brainsets prepare <brainset>

Data preparation involves downloading the raw data from the source then processing it, following a set of rules defined in pipelines/<brainset>/. For example, to prepare the Perich & Miller (2018) dataset, you can run:

brainsets prepare perich_miller_population_2018 --cores 8