Missing MRI Algorithms

The following classes provide algorithms from the BraTS Global synthesis challenge to predict missing MRI modalities.

class brats.core.missing_mri_algorithms.MissingMRI(algorithm: MissingMRIAlgorithms = MissingMRIAlgorithms.BraTS24_1, cuda_devices: str | None = '0', force_cpu: bool = False)

Bases: BraTSAlgorithm

infer_batch(data_folder: Path | str, output_folder: Path | str, log_file: Path | str | None = None, backend: Backends | None = Backends.DOCKER) → None

Perform synthesis on a batch of subjects with the provided images and save the results to the output folder.

Requires the following structure (if e.g. t2f should be synthesized):

data_folder

┣ A

┃ ┣ A-t1c.nii.gz

┃ ┣ A-t1n.nii.gz

┃ ┗ A-t2w.nii.gz

┣ B

┃ ┣ B-t1c.nii.gz

┃ ┣ …

Parameters:

  • data_folder (Path | str) – Folder containing the subjects with required structure

  • output_folder (Path | str) – Output folder to save the segmentation

  • log_file (Path | str, optional) – Save logs to this file

  • backend (Backends, optional) – Backend to use for inference. Defaults to Backends.DOCKER.

infer_single(output_file: Path | str, t1c: Path | str | None = None, t1n: Path | str | None = None, t2f: Path | str | None = None, t2w: Path | str | None = None, log_file: Path | str | None = None, backend: Backends | None = Backends.DOCKER) → None

Perform synthesis of the missing modality for a single subject with the provided images and save the result to the output file.

Note

Exactly 3 input modalities are required to perform synthesis of the missing modality.

Parameters:

  • output_file (Path | str) – Output file to save the synthesized image

  • t1c (Optional[Union[Path, str]], optional) – Path to the T1c image. Defaults to None.

  • t1n (Optional[Union[Path, str]], optional) – Path to the T1n image. Defaults to None.

  • t2f (Optional[Union[Path, str]], optional) – Path to the T2f image. Defaults to None.

  • t2w (Optional[Union[Path, str]], optional) – Path to the T2w image. Defaults to None.

  • log_file (Optional[Path | str], optional) – Save logs to this file. Defaults to None.

  • backend (Backends, optional) – Backend to use for inference. Defaults to Backends.DOCKER.