3. Command Line Interface

brainprep is a command-line interface for running brain imaging preprocessing workflows.

3.1. Introduction

brainprep provides a dynamic, Fire-powered command-line interface that automatically exposes all workflows and interfaces as CLI commands. It also injects global configuration parameters into each workflow function signature, enabling users to override default processing options directly from the command line.

3.2. Usage

brainprep [WORKFLOW] [WORKFLOW PARAMS] [CONFIG PARAMS]

[WORKFLOW] specifies which preprocessing pipeline to run, [WORKFLOW PARAMS] are the input arguments associated with that workflow, and [CONFIG PARAMS] are the arguments associated with the context manager.

Use brainprep --help to list all available workflows, or brainprep [WORKFLOW] --help to display the parameters required by a specific workflow.

brainprep interface [INTERFACE] [INTERFACE PARAMS] [CONFIG PARAMS]

[INTERFACE] specifies which interface to run, [INTERFACE PARAMS] are the input arguments associated with that interface, and [CONFIG PARAMS] are the arguments associated with the context manager.

Use brainprep interface --help to list all available workflows, or brainprep interface [INTERFACE] --help to display the parameters required by a specific interface.