pyalfe.tasks.skullstripping

class pyalfe.tasks.skullstripping.Skullstripping(inference_model: InferenceModel, image_processor: ImageProcessor, pipeline_dir: PipelineDataDir, modalities: list[Modality], overwrite: bool = True)

Bases: Task

This task performs skullstripping for all the modalities.

inference_model

The inference model object.

Type:

InferenceModel

image_processor

The image processor object.

Type:

ImageProcessor

pipeline_dir

The pipeline data directory object.

Type:

PipelineDataDir

modalities

All the modalities that should be skullstripped.

Type:

list[Modality]

overwrite

Whether to overwrite any existing output image. Default is True.

Type:

bool

logger = <Logger Skullstripping (DEBUG)>

process_modalities(accession, modalities)

run(accession)

Runs the task for an accession.