from brats_toolkit.preprocessor import Preprocessor

# instantiate

prep = Preprocessor()

# define inputs and outputs

inputDir = "example_data/input_preprocessor_batch_processing/exams_to_preprocess"

outputDir = "example_data/output_preprocessor_batch"

# execute it

prep.batch_preprocess(

    exam_import_folder=inputDir,

    exam_export_folder=outputDir,

    # this way the brain extraction will run on gpu

    mode="gpu",

    confirm=True,

    skipUpdate=False,

    gpuid="0",

)