Usage

You can use bids2openminds as both a command line tool and a python library.

Usage as Python library

Overview

The convert function processes a Brain Imaging Data Structure (BIDS) directory, converts its contents into OpenMINDS format, and optionally saves the output. It handles BIDS layout, extracts relevant information, and creates a dataset description based on BIDS data using OpenMINDS templates.

Function Signature

>>> def convert(input_path, save_output=False, output_path=None, multiple_files=False, include_empty_properties=False, quiet=False):

Parameters

input_path (str): Path to the BIDS directory. This is required and must be a valid directory.
save_output (bool, default=False): If True, the converted OpenMINDS data will be saved to the specified output_path.
output_path (str, default=None): The path where the OpenMINDS data should be saved. If not specified, defaults to [input_path]/openminds.jsonld (single file mode) or [input_path]/openminds/ (multiple files mode).
multiple_files (bool, default=False): If True, the OpenMINDS data will be saved into multiple files within the specified output_path.
include_empty_properties (bool, default=False): If True, includes all the openMINDS properties with empty values in the final output. Otherwise includes only properties that have a non None value.
quiet (bool, default=False): If True, suppresses warnings and the final report output. Only prints success messages.

Returns

collection (openminds.Collection): The OpenMINDS collection object representing the converted dataset. For more information on OpenMINDS collection please refer to openMINDS readthedocs.

Example Usage

>>> import bids2openminds.converter as converter
>>> input_path = "/path/to/BIDS/dataset"
>>> collection = converter.convert(input_path, save_output=True, output_path="/path/to/output", multiple_files=False, include_empty_properties=False, quiet=False)

Or one can chose the default parmetrs as following:

>>> import bids2openminds.converter as converter
>>> collection = converter.convert("/path/to/BIDS/dataset")

Command-Line Interface (CLI)

This function is also accessible via a command-line interface using the click library.

Usage: bids2openminds [OPTIONS] INPUT_PATH

Arguments:
    input-path   Path to the BIDS directory.

Options:
    -o, --output-path PATH      The output path or filename for OpenMINDS file/files.
    --single-file               Save the entire collection into a single file (default).
    --multiple-files            Save each node into a separate file within the specified directory.
    -e, --include-empty-properties
                                Include empty properties in the final file.
    -q, --quiet                 Suppress warnings and reports.