data_import module

load_data

Reads and optionally converts dataset into ASL-BIDS format. It ensures data adherence to the BIDS format and handles conversion using user-defined parameters.

load_data(root: str, params_json: str, convert=True, is_singledelay=True, is_labelcontrol=True)

Parameters:

root (str): The root directory of the dataset.
params_json (str): Path to the JSON file containing user-defined parameters (see JSON Parameters section in Tutorials).
convert (bool, optional): Flag indicating whether to convert data to ASL-BIDS format. Default is True.
is_singledelay (bool, optional): Flag indicating whether the ASL data is single-delay.
is_labelcontrol (bool, optional): Flag indicating whether the ASL data is arranged in a label-first order.

Outputs:

The original dataset will be renamed as rawdata_user and the converted ASL-BIDS dataset will be stored as rawdata under root. A data_description.json file is also generated under root to store some basic information about the dataset.

check_bids_format

Verifies if a given root path follows the pre-required BIDS format. It checks the presence and structure of necessary directories and files within the dataset.

check_bids_format(root: str)

Parameters:

root (str): The root directory of the dataset.

Returns:

valid (bool): Flag indicating whether this function runs without error.
error (str): Error information.
img_type (str): Image file format (.nii or .img).
has_structural (bool): Flag indicating whether the dataset has structural images.

read_params

Reads and validates user-defined parameters from a JSON file. It ensures that all necessary parameters for ASL data processing are present and correctly formatted.

read_params(params_json: str, has_structural: bool, is_singledelay: bool)

Parameters:

params_json (str): Path to the JSON file containing user-defined parameters.
has_structural (bool): Whether the directory has structural images.
is_singledelay (bool): Flag indicating whether the ASL data is single-delay.

Returns:

valid (bool): Flag indicating whether this function runs without error.
error (str): Error information.
params (dict): Parameters read from the JSON file.

make_sidecar

Generates JSON sidecar files for ASL and structural MRI data, as well as a TSV file containing aslcontext information. It processes user-defined parameters and organizes them into the appropriate formats for ASL-BIDS compliance.

make_sidecar(params: dict, num_volumes: int, is_singledelay: bool, is_labelcontrol: bool)

Parameters:

params (dict): Parameters read from the user-input JSON file.
num_volumes (int): Number of volumes in the ASL image.
is_singledelay (bool): Flag indicating whether the ASL data is single-delay.
is_labelcontrol (bool): Flag indicating whether the ASL data is arranged in a label-first order.

Returns:

asl_json_data (dict): Sidecar information for ASL images.
structural_json_data (dict): Sidecar information for structural images.
tsv_data (dict): ASL context.

convert2bids

Converts MRI data from its original format into the ASL-BIDS format. It processes ASL and structural images, converting them to NIfTI format if necessary, and generates associated sidecar files.

convert2bids(root: str, params: dict, img_type: str, has_structural: bool, is_singledelay: bool, is_labelcontrol: bool)

Parameters:

root (str): The root directory of the dataset.
params (dict): Parameters read from the user-input JSON file.
img_type (str): Image file format (.nii or .img).
has_structural (bool): Flag indicating whether the dataset has structural images.
is_singledelay (bool): Flag indicating whether the ASL data is single-delay.
is_labelcontrol (bool): Flag indicating whether the ASL data is arranged in a label-first order.

Returns:

valid (bool): Flag indicating whether this function runs without error.
error (str): Error information.

Outputs:

The original dataset will be renamed as rawdata_user. The converted ASL-BIDS dataset with NIFTI images and sidecar files will be stored as rawdata under root. A data_description.json file is also generated under root to store some basic information about the dataset.

read_asl_bids

Reads data from an ASL-BIDS-compliant dataset. It extracts relevant metadata and organizes it into a data description JSON file.

read_asl_bids(root: str, img_type: str, has_structural: bool)

Parameters:

root (str): The root directory of the dataset.
img_type (str): Image file format (.nii or .img).
has_structural (bool): Flag indicating whether the dataset has structural images.

Outputs:

A data_description.json file under root to store some basic information about the dataset.

create_derivatives_folders

Creates the derivatives folders for the ASL MRI dataset based on the provided data description.

create_derivatives_folders(data_descrip: dict)

Parameters:

data_descrip (dict): A dictionary containing the data description, which includes information about the images and their paths.

Outputs:

Creates the derivatives folder under root, with the same subject, session, and modality subfolders as rawdata.