brats_toolkit package

class brats_toolkit.fusionator.Fusionator(**kwargs)

Bases: object

fuse(segmentations, outputPath, method='mav', weights=None, labels=None)
Parameters:

  • segmentations ([type]) – [description]

  • outputPath ([type]) – [description]

  • method (str, optional) – [description]. Defaults to ‘mav’.

  • weights ([type], optional) – [description]. Defaults to None.

Raises:

IOError – [description]

class brats_toolkit.preprocessor.Preprocessor(**kwargs)

Bases: object

Class for preprocessing medical imaging data.

batch_preprocess(exam_import_folder: str, exam_export_folder: str, dicom_import_folder: str | None = None, nifti_export_folder: str | None = None, mode: str = 'cpu', confirm: bool = True, skipUpdate: bool = False, gpuid: str = '0') → None

Process multiple sets of input files, potentially using Docker.

Parameters: - exam_import_folder (str): Import folder path. - exam_export_folder (str): Export folder path. - dicom_import_folder (Optional[str]): DICOM import folder path. - nifti_export_folder (Optional[str]): NIfTI export folder path. - mode (str): Processing mode (e.g., “cpu”, “gpu”). - confirm (bool): Whether confirmation is required. - skipUpdate (bool): Whether to skip Docker update. - gpuid (str): GPU ID.

Returns: - None

single_preprocess(t1File: str, t1cFile: str, t2File: str, flaFile: str, outputFolder: str, mode: str, confirm: bool = False, skipUpdate: bool = False, gpuid: str = '0') → None

Process a single set of input files.

Parameters: - t1File (str): Path to T1 file. - t1cFile (str): Path to T1c file. - t2File (str): Path to T2 file. - flaFile (str): Path to FLAIR file. - outputFolder (str): Output folder path. - mode (str): Processing mode (e.g., “cpu”, “gpu”). - confirm (bool): Whether confirmation is required. - skipUpdate (bool): Whether to skip Docker update. - gpuid (str): GPU ID.

Returns: - None

class brats_toolkit.segmentor.Segmentor(**kwargs)

Bases: object

Now does it all!

segment(t1=None, t1c=None, t2=None, fla=None, cid='mocker', outputPath=None)
Parameters:

  • t1 ([type], optional) – [description]. Defaults to None.

  • t1c ([type], optional) – [description]. Defaults to None.

  • t2 ([type], optional) – [description]. Defaults to None.

  • fla ([type], optional) – [description]. Defaults to None.

  • cid (str, optional) – [description]. Defaults to ‘mocker’.

  • outputPath ([type], optional) – [description]. Defaults to None.