oxford_asl module

run_oxford_asl

Executes the oxford_asl command-line tool to process ASL MRI data, incorporating various options for calibration, motion correction, and other image processing features.

run_oxford_asl(
    root: str,
    useStructural=False,
    useCalibration=False,
    cmethod="voxel",
    wp=False,
    mc=False,
    bat=None,
    t1=None,
    t1b=None,
    sliceband=None,
)

Parameters:

  • root (str): The root directory where the dataset is located.

  • useStructural (bool, optional): If True, uses structural images for processing. Default is False.

  • useCalibration (bool, optional): If True, includes calibration in the processing steps. Default is False.

  • cmethod (str, optional): Calibration method, either "voxel" or "single". Default is "voxel".

  • wp (bool, optional): If True, do analysis in ‘White Paper Mode’. Default is False.

  • mc (bool, optional): If True, applies motion correction. Default is False.

  • bat (float, optional): Bolus arrival time (in seconds).

  • t1 (float, optional): T1 value of tissue (in seconds).

  • t1b (float, optional): T1 value of arterial blood (in seconds).

  • sliceband (int, optional): Number of slices per band in a multi-band acquisition.

Raises:

  • ValueError: If using "single" calibration method without structural images, or if required structural or calibration images are missing.

Outputs:

Output folders are stored in each session under derivatives. For output file details, please refer to the Oxford ASL documentation.

split_asl_m0

When M0Type=Included, this function splits ASL and M0 images from a single file based on ASL context information, saving them as individual NIfTI images.

split_asl_m0(file_path: str, asl_context: list)

Parameters:

  • file_path (str): The path to the 4D MRI file containing combined ASL and M0 scans.

  • asl_context (list): A list indicating the context of each volume within the file, specifying which are ASL scans and which are M0 scans.

Returns:

  • A tuple containing two elements:

    • asl_path (str): The file path where the separated ASL data is saved.

    • m0_path (str): The file path where the separated M0 data is saved.