monai-weekly 1.5.dev2514__tar.gz → 1.5.dev2516__tar.gz

{monai_weekly-1.5.dev2514/monai_weekly.egg-info → monai_weekly-1.5.dev2516}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.5.dev2514
+Version: 1.5.dev2516
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -49,6 +49,7 @@ Requires-Dist: lmdb; extra == "all"
 Requires-Dist: psutil; extra == "all"
 Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "all"
 Requires-Dist: openslide-python; extra == "all"
+Requires-Dist: openslide-bin; extra == "all"
 Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
 Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
 Requires-Dist: pandas; extra == "all"
@@ -105,6 +106,7 @@ Provides-Extra: cucim
 Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "cucim"
 Provides-Extra: openslide
 Requires-Dist: openslide-python; extra == "openslide"
+Requires-Dist: openslide-bin; extra == "openslide"
 Provides-Extra: tifffile
 Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "tifffile"
 Provides-Extra: imagecodecs

{monai_weekly-1.5.dev2514 → monai_weekly-1.5.dev2516}/monai/__init__.py

@@ -136,4 +136,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "4986d7ffd2d351c9d66de0e0329884b1a26d5500"
+__commit_id__ = "b58e883c887e0f99d382807550654c44d94f47bd"

{monai_weekly-1.5.dev2514 → monai_weekly-1.5.dev2516}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-04-06T02:31:51+0000",
+ "date": "2025-04-20T02:32:55+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "a3ea49fc4e600d131daadad61ea340df25fcfdaa",
- "version": "1.5.dev2514"
+ "full-revisionid": "875aa3d53281b83a205442db83ac41ddf817ef9a",
+ "version": "1.5.dev2516"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.5.dev2514 → monai_weekly-1.5.dev2516}/monai/apps/nnunet/__init__.py

@@ -11,5 +11,13 @@
 
 from __future__ import annotations
 
+from .nnunet_bundle import (
+    ModelnnUNetWrapper,
+    convert_monai_bundle_to_nnunet,
+    convert_nnunet_to_monai_bundle,
+    get_network_from_nnunet_plans,
+    get_nnunet_monai_predictor,
+    get_nnunet_trainer,
+)
 from .nnunetv2_runner import nnUNetV2Runner
 from .utils import NNUNETMode, analyze_data, create_new_data_copy, create_new_dataset_json

monai_weekly-1.5.dev2516/monai/apps/nnunet/nnunet_bundle.py

@@ -0,0 +1,594 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+from __future__ import annotations
+
+import os
+import shutil
+from pathlib import Path
+from typing import Any, Optional, Union
+
+import numpy as np
+import torch
+from torch.backends import cudnn
+
+from monai.data.meta_tensor import MetaTensor
+from monai.utils import optional_import
+
+join, _ = optional_import("batchgenerators.utilities.file_and_folder_operations", name="join")
+load_json, _ = optional_import("batchgenerators.utilities.file_and_folder_operations", name="load_json")
+
+__all__ = [
+    "get_nnunet_trainer",
+    "get_nnunet_monai_predictor",
+    "get_network_from_nnunet_plans",
+    "convert_nnunet_to_monai_bundle",
+    "convert_monai_bundle_to_nnunet",
+    "ModelnnUNetWrapper",
+]
+
+
+def get_nnunet_trainer(
+    dataset_name_or_id: Union[str, int],
+    configuration: str,
+    fold: Union[int, str],
+    trainer_class_name: str = "nnUNetTrainer",
+    plans_identifier: str = "nnUNetPlans",
+    use_compressed_data: bool = False,
+    continue_training: bool = False,
+    only_run_validation: bool = False,
+    disable_checkpointing: bool = False,
+    device: str = "cuda",
+    pretrained_model: Optional[str] = None,
+) -> Any:  # type: ignore
+    """
+    Get the nnUNet trainer instance based on the provided configuration.
+    The returned nnUNet trainer can be used to initialize the SupervisedTrainer for training, including the network,
+    optimizer, loss function, DataLoader, etc.
+
+    Example::
+
+        from monai.apps import SupervisedTrainer
+        from monai.bundle.nnunet import get_nnunet_trainer
+
+        dataset_name_or_id = 'Task009_Spleen'
+        fold = 0
+        configuration = '3d_fullres'
+        nnunet_trainer = get_nnunet_trainer(dataset_name_or_id, configuration, fold)
+
+        trainer = SupervisedTrainer(
+            device=nnunet_trainer.device,
+            max_epochs=nnunet_trainer.num_epochs,
+            train_data_loader=nnunet_trainer.dataloader_train,
+            network=nnunet_trainer.network,
+            optimizer=nnunet_trainer.optimizer,
+            loss_function=nnunet_trainer.loss_function,
+            epoch_length=nnunet_trainer.num_iterations_per_epoch,
+        )
+
+    Parameters
+    ----------
+    dataset_name_or_id : Union[str, int]
+        The name or ID of the dataset to be used.
+    configuration : str
+        The configuration name for the training.
+    fold : Union[int, str]
+        The fold number or 'all' for cross-validation.
+    trainer_class_name : str, optional
+        The class name of the trainer to be used. Default is 'nnUNetTrainer'.
+        For a complete list of supported trainers, check:
+        https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunetv2/training/nnUNetTrainer/variants
+    plans_identifier : str, optional
+        Identifier for the plans to be used. Default is 'nnUNetPlans'.
+    use_compressed_data : bool, optional
+        Whether to use compressed data. Default is False.
+    continue_training : bool, optional
+        Whether to continue training from a checkpoint. Default is False.
+    only_run_validation : bool, optional
+        Whether to only run validation. Default is False.
+    disable_checkpointing : bool, optional
+        Whether to disable checkpointing. Default is False.
+    device : str, optional
+        The device to be used for training. Default is 'cuda'.
+    pretrained_model : Optional[str], optional
+        Path to the pretrained model file.
+
+    Returns
+    -------
+    nnunet_trainer : object
+        The nnUNet trainer instance.
+    """
+    # From nnUNet/nnunetv2/run/run_training.py#run_training
+    if isinstance(fold, str):
+        if fold != "all":
+            try:
+                fold = int(fold)
+            except ValueError as e:
+                print(
+                    f'Unable to convert given value for fold to int: {fold}. fold must bei either "all" or an integer!'
+                )
+                raise e
+
+    from nnunetv2.run.run_training import get_trainer_from_args, maybe_load_checkpoint
+
+    nnunet_trainer = get_trainer_from_args(
+        str(dataset_name_or_id), configuration, fold, trainer_class_name, plans_identifier, device=torch.device(device)
+    )
+    if disable_checkpointing:
+        nnunet_trainer.disable_checkpointing = disable_checkpointing
+
+    assert not (continue_training and only_run_validation), "Cannot set --c and --val flag at the same time. Dummy."
+
+    maybe_load_checkpoint(nnunet_trainer, continue_training, only_run_validation)
+    nnunet_trainer.on_train_start()  # Added to Initialize Trainer
+    if torch.cuda.is_available():
+        cudnn.deterministic = False
+        cudnn.benchmark = True
+
+    if pretrained_model is not None:
+        state_dict = torch.load(pretrained_model)
+        if "network_weights" in state_dict:
+            nnunet_trainer.network._orig_mod.load_state_dict(state_dict["network_weights"])
+    return nnunet_trainer
+
+
+class ModelnnUNetWrapper(torch.nn.Module):
+    """
+    A wrapper class for nnUNet model integration with MONAI framework.
+    The wrapper can be use to integrate the nnUNet Bundle within MONAI framework for inference.
+
+    Parameters
+    ----------
+    predictor : nnUNetPredictor
+        The nnUNet predictor object used for inference.
+    model_folder : Union[str, Path]
+        The folder path where the model and related files are stored.
+    model_name : str, optional
+        The name of the model file, by default "model.pt".
+
+    Attributes
+    ----------
+    predictor : nnUNetPredictor
+        The nnUNet predictor object used for inference.
+    network_weights : torch.nn.Module
+        The network weights of the model.
+
+    Notes
+    -----
+    This class integrates nnUNet model with MONAI framework by loading necessary configurations,
+    restoring network architecture, and setting up the predictor for inference.
+    """
+
+    def __init__(self, predictor: object, model_folder: Union[str, Path], model_name: str = "model.pt"):  # type: ignore
+        super().__init__()
+        self.predictor = predictor
+
+        model_training_output_dir = model_folder
+
+        from nnunetv2.utilities.plans_handling.plans_handler import PlansManager
+
+        # Block Added from nnUNet/nnunetv2/inference/predict_from_raw_data.py#nnUNetPredictor
+        dataset_json = load_json(join(Path(model_training_output_dir).parent, "dataset.json"))
+        plans = load_json(join(Path(model_training_output_dir).parent, "plans.json"))
+        plans_manager = PlansManager(plans)
+
+        parameters = []
+
+        checkpoint = torch.load(
+            join(Path(model_training_output_dir).parent, "nnunet_checkpoint.pth"), map_location=torch.device("cpu")
+        )
+        trainer_name = checkpoint["trainer_name"]
+        configuration_name = checkpoint["init_args"]["configuration"]
+        inference_allowed_mirroring_axes = (
+            checkpoint["inference_allowed_mirroring_axes"]
+            if "inference_allowed_mirroring_axes" in checkpoint.keys()
+            else None
+        )
+        if Path(model_training_output_dir).joinpath(model_name).is_file():
+            monai_checkpoint = torch.load(join(model_training_output_dir, model_name), map_location=torch.device("cpu"))
+            if "network_weights" in monai_checkpoint.keys():
+                parameters.append(monai_checkpoint["network_weights"])
+            else:
+                parameters.append(monai_checkpoint)
+
+        configuration_manager = plans_manager.get_configuration(configuration_name)
+        import nnunetv2
+        from nnunetv2.utilities.find_class_by_name import recursive_find_python_class
+        from nnunetv2.utilities.label_handling.label_handling import determine_num_input_channels
+
+        num_input_channels = determine_num_input_channels(plans_manager, configuration_manager, dataset_json)
+        trainer_class = recursive_find_python_class(
+            join(nnunetv2.__path__[0], "training", "nnUNetTrainer"), trainer_name, "nnunetv2.training.nnUNetTrainer"
+        )
+        if trainer_class is None:
+            raise RuntimeError(
+                f"Unable to locate trainer class {trainer_name} in nnunetv2.training.nnUNetTrainer. "
+                f"Please place it there (in any .py file)!"
+            )
+        network = trainer_class.build_network_architecture(
+            configuration_manager.network_arch_class_name,
+            configuration_manager.network_arch_init_kwargs,
+            configuration_manager.network_arch_init_kwargs_req_import,
+            num_input_channels,
+            plans_manager.get_label_manager(dataset_json).num_segmentation_heads,
+            enable_deep_supervision=False,
+        )
+
+        predictor.plans_manager = plans_manager  # type: ignore
+        predictor.configuration_manager = configuration_manager  # type: ignore
+        predictor.list_of_parameters = parameters  # type: ignore
+        predictor.network = network  # type: ignore
+        predictor.dataset_json = dataset_json  # type: ignore
+        predictor.trainer_name = trainer_name  # type: ignore
+        predictor.allowed_mirroring_axes = inference_allowed_mirroring_axes  # type: ignore
+        predictor.label_manager = plans_manager.get_label_manager(dataset_json)  # type: ignore
+
+        self.network_weights = self.predictor.network  # type: ignore
+
+    def forward(self, x: MetaTensor) -> MetaTensor:
+        """
+        Forward pass for the nnUNet model.
+
+        Args:
+            x (MetaTensor): Input tensor. If the input is a tuple,
+                it is assumed to be a decollated batch (list of tensors). Otherwise, it is assumed to be a collated batch.
+
+        Returns:
+            MetaTensor: The output tensor with the same metadata as the input.
+
+        Raises:
+            TypeError: If the input is not a torch.Tensor or a tuple of MetaTensors.
+
+        Notes:
+            - If the input is a tuple, the filenames are extracted from the metadata of each tensor in the tuple.
+            - If the input is a collated batch, the filenames are extracted from the metadata of the input tensor.
+            - The filenames are used to generate predictions using the nnUNet predictor.
+            - The predictions are converted to torch tensors, with added batch and channel dimensions.
+            - The output tensor is concatenated along the batch dimension and returned as a MetaTensor with the same metadata.
+        """
+        if isinstance(x, MetaTensor):
+            if "pixdim" in x.meta:
+                properties_or_list_of_properties = {"spacing": x.meta["pixdim"][0][1:4].numpy().tolist()}
+            elif "affine" in x.meta:
+                spacing = [
+                    abs(x.meta["affine"][0][0].item()),
+                    abs(x.meta["affine"][1][1].item()),
+                    abs(x.meta["affine"][2][2].item()),
+                ]
+                properties_or_list_of_properties = {"spacing": spacing}
+            else:
+                properties_or_list_of_properties = {"spacing": [1.0, 1.0, 1.0]}
+        else:
+            raise TypeError("Input must be a MetaTensor or a tuple of MetaTensors.")
+
+        image_or_list_of_images = x.cpu().numpy()[0, :]
+
+        # input_files should be a list of file paths, one per modality
+        prediction_output = self.predictor.predict_from_list_of_npy_arrays(  # type: ignore
+            image_or_list_of_images,
+            None,
+            properties_or_list_of_properties,
+            truncated_ofname=None,
+            save_probabilities=False,
+            num_processes=2,
+            num_processes_segmentation_export=2,
+        )
+        # prediction_output is a list of numpy arrays, with dimensions (H, W, D), output from ArgMax
+
+        out_tensors = []
+        for out in prediction_output:  # Add batch and channel dimensions
+            out_tensors.append(torch.from_numpy(np.expand_dims(np.expand_dims(out, 0), 0)))
+        out_tensor = torch.cat(out_tensors, 0)  # Concatenate along batch dimension
+
+        return MetaTensor(out_tensor, meta=x.meta)
+
+
+def get_nnunet_monai_predictor(model_folder: Union[str, Path], model_name: str = "model.pt") -> ModelnnUNetWrapper:
+    """
+    Initializes and returns a `nnUNetMONAIModelWrapper` containing the corresponding `nnUNetPredictor`.
+    The model folder should contain the following files, created during training:
+
+        - dataset.json: from the nnUNet results folder
+        - plans.json: from the nnUNet results folder
+        - nnunet_checkpoint.pth: The nnUNet checkpoint file, containing the nnUNet training configuration
+        - model.pt: The checkpoint file containing the model weights.
+
+    The returned wrapper object can be used for inference with MONAI framework:
+
+    Example::
+
+        from monai.bundle.nnunet import get_nnunet_monai_predictor
+
+        model_folder = 'path/to/monai_bundle/model'
+        model_name = 'model.pt'
+        wrapper = get_nnunet_monai_predictor(model_folder, model_name)
+
+        # Perform inference
+        input_data = ...
+        output = wrapper(input_data)
+
+
+    Parameters
+    ----------
+    model_folder : Union[str, Path]
+        The folder where the model is stored.
+    model_name : str, optional
+        The name of the model file, by default "model.pt".
+
+    Returns
+    -------
+    ModelnnUNetWrapper
+        A wrapper object that contains the nnUNetPredictor and the loaded model.
+    """
+
+    from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
+
+    predictor = nnUNetPredictor(
+        tile_step_size=0.5,
+        use_gaussian=True,
+        use_mirroring=False,
+        device=torch.device("cuda", 0),
+        verbose=False,
+        verbose_preprocessing=False,
+        allow_tqdm=True,
+    )
+    # initializes the network architecture, loads the checkpoint
+    wrapper = ModelnnUNetWrapper(predictor, model_folder, model_name)
+    return wrapper
+
+
+def convert_nnunet_to_monai_bundle(nnunet_config: dict, bundle_root_folder: str, fold: int = 0) -> None:
+    """
+    Convert nnUNet model checkpoints and configuration to MONAI bundle format.
+
+    Parameters
+    ----------
+    nnunet_config : dict
+        Configuration dictionary for nnUNet, containing keys such as 'dataset_name_or_id', 'nnunet_configuration',
+        'nnunet_trainer', and 'nnunet_plans'.
+    bundle_root_folder : str
+        Root folder where the MONAI bundle will be saved.
+    fold : int, optional
+        Fold number of the nnUNet model to be converted, by default 0.
+
+    Returns
+    -------
+    None
+    """
+
+    nnunet_trainer = "nnUNetTrainer"
+    nnunet_plans = "nnUNetPlans"
+    nnunet_configuration = "3d_fullres"
+
+    if "nnunet_trainer" in nnunet_config:
+        nnunet_trainer = nnunet_config["nnunet_trainer"]
+
+    if "nnunet_plans" in nnunet_config:
+        nnunet_plans = nnunet_config["nnunet_plans"]
+
+    if "nnunet_configuration" in nnunet_config:
+        nnunet_configuration = nnunet_config["nnunet_configuration"]
+
+    from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name
+
+    dataset_name = maybe_convert_to_dataset_name(nnunet_config["dataset_name_or_id"])
+    nnunet_model_folder = Path(os.environ["nnUNet_results"]).joinpath(
+        dataset_name, f"{nnunet_trainer}__{nnunet_plans}__{nnunet_configuration}"
+    )
+
+    nnunet_checkpoint_final = torch.load(Path(nnunet_model_folder).joinpath(f"fold_{fold}", "checkpoint_final.pth"))
+    nnunet_checkpoint_best = torch.load(Path(nnunet_model_folder).joinpath(f"fold_{fold}", "checkpoint_best.pth"))
+
+    nnunet_checkpoint = {}
+    nnunet_checkpoint["inference_allowed_mirroring_axes"] = nnunet_checkpoint_final["inference_allowed_mirroring_axes"]
+    nnunet_checkpoint["init_args"] = nnunet_checkpoint_final["init_args"]
+    nnunet_checkpoint["trainer_name"] = nnunet_checkpoint_final["trainer_name"]
+
+    torch.save(nnunet_checkpoint, Path(bundle_root_folder).joinpath("models", "nnunet_checkpoint.pth"))
+
+    Path(bundle_root_folder).joinpath("models", f"fold_{fold}").mkdir(parents=True, exist_ok=True)
+    monai_last_checkpoint = {}
+    monai_last_checkpoint["network_weights"] = nnunet_checkpoint_final["network_weights"]
+    torch.save(monai_last_checkpoint, Path(bundle_root_folder).joinpath("models", f"fold_{fold}", "model.pt"))
+
+    monai_best_checkpoint = {}
+    monai_best_checkpoint["network_weights"] = nnunet_checkpoint_best["network_weights"]
+    torch.save(monai_best_checkpoint, Path(bundle_root_folder).joinpath("models", f"fold_{fold}", "best_model.pt"))
+
+    if not os.path.exists(os.path.join(bundle_root_folder, "models", "plans.json")):
+        shutil.copy(
+            Path(nnunet_model_folder).joinpath("plans.json"), Path(bundle_root_folder).joinpath("models", "plans.json")
+        )
+
+    if not os.path.exists(os.path.join(bundle_root_folder, "models", "dataset.json")):
+        shutil.copy(
+            Path(nnunet_model_folder).joinpath("dataset.json"),
+            Path(bundle_root_folder).joinpath("models", "dataset.json"),
+        )
+
+
+def get_network_from_nnunet_plans(
+    plans_file: str,
+    dataset_file: str,
+    configuration: str,
+    model_ckpt: Optional[str] = None,
+    model_key_in_ckpt: str = "model",
+) -> Union[torch.nn.Module, Any]:
+    """
+    Load and initialize a nnUNet network based on nnUNet plans and configuration.
+
+    Parameters
+    ----------
+    plans_file : str
+        Path to the JSON file containing the nnUNet plans.
+    dataset_file : str
+        Path to the JSON file containing the dataset information.
+    configuration : str
+        The configuration name to be used from the plans.
+    model_ckpt : Optional[str], optional
+        Path to the model checkpoint file. If None, the network is returned without loading weights (default is None).
+    model_key_in_ckpt : str, optional
+        The key in the checkpoint file that contains the model state dictionary (default is "model").
+
+    Returns
+    -------
+    network : torch.nn.Module
+        The initialized neural network, with weights loaded if `model_ckpt` is provided.
+    """
+    from batchgenerators.utilities.file_and_folder_operations import load_json
+    from nnunetv2.utilities.get_network_from_plans import get_network_from_plans
+    from nnunetv2.utilities.label_handling.label_handling import determine_num_input_channels
+    from nnunetv2.utilities.plans_handling.plans_handler import PlansManager
+
+    plans = load_json(plans_file)
+    dataset_json = load_json(dataset_file)
+
+    plans_manager = PlansManager(plans)
+    configuration_manager = plans_manager.get_configuration(configuration)
+    num_input_channels = determine_num_input_channels(plans_manager, configuration_manager, dataset_json)
+    label_manager = plans_manager.get_label_manager(dataset_json)
+
+    enable_deep_supervision = True
+
+    network = get_network_from_plans(
+        configuration_manager.network_arch_class_name,
+        configuration_manager.network_arch_init_kwargs,
+        configuration_manager.network_arch_init_kwargs_req_import,
+        num_input_channels,
+        label_manager.num_segmentation_heads,
+        allow_init=True,
+        deep_supervision=enable_deep_supervision,
+    )
+
+    if model_ckpt is None:
+        return network
+    else:
+        state_dict = torch.load(model_ckpt)
+        network.load_state_dict(state_dict[model_key_in_ckpt])
+        return network
+
+
+def convert_monai_bundle_to_nnunet(nnunet_config: dict, bundle_root_folder: str, fold: int = 0) -> None:
+    """
+    Convert a MONAI bundle to nnU-Net format.
+
+    Parameters
+    ----------
+    nnunet_config : dict
+        Configuration dictionary for nnU-Net. Expected keys are:
+        - "dataset_name_or_id": str, name or ID of the dataset.
+        - "nnunet_trainer": str, optional, name of the nnU-Net trainer (default is "nnUNetTrainer").
+        - "nnunet_plans": str, optional, name of the nnU-Net plans (default is "nnUNetPlans").
+    bundle_root_folder : str
+        Path to the root folder of the MONAI bundle.
+    fold : int, optional
+        Fold number for cross-validation (default is 0).
+
+    Returns
+    -------
+    None
+    """
+    from odict import odict
+
+    nnunet_trainer: str = "nnUNetTrainer"
+    nnunet_plans: str = "nnUNetPlans"
+
+    if "nnunet_trainer" in nnunet_config:
+        nnunet_trainer = nnunet_config["nnunet_trainer"]
+
+    if "nnunet_plans" in nnunet_config:
+        nnunet_plans = nnunet_config["nnunet_plans"]
+
+    from nnunetv2.training.logging.nnunet_logger import nnUNetLogger
+    from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name
+
+    def subfiles(
+        folder: Union[str, Path], prefix: Optional[str] = None, suffix: Optional[str] = None, sort: bool = True
+    ) -> list[str]:
+        res = [
+            i.name
+            for i in Path(folder).iterdir()
+            if i.is_file()
+            and (prefix is None or i.name.startswith(prefix))
+            and (suffix is None or i.name.endswith(suffix))
+        ]
+        if sort:
+            res.sort()
+        return res
+
+    nnunet_model_folder: Path = Path(os.environ["nnUNet_results"]).joinpath(
+        maybe_convert_to_dataset_name(nnunet_config["dataset_name_or_id"]),
+        f"{nnunet_trainer}__{nnunet_plans}__3d_fullres",
+    )
+
+    nnunet_preprocess_model_folder: Path = Path(os.environ["nnUNet_preprocessed"]).joinpath(
+        maybe_convert_to_dataset_name(nnunet_config["dataset_name_or_id"])
+    )
+
+    Path(nnunet_model_folder).joinpath(f"fold_{fold}").mkdir(parents=True, exist_ok=True)
+
+    nnunet_checkpoint: dict = torch.load(f"{bundle_root_folder}/models/nnunet_checkpoint.pth")
+    latest_checkpoints: list[str] = subfiles(
+        Path(bundle_root_folder).joinpath("models", f"fold_{fold}"), prefix="checkpoint_epoch", sort=True
+    )
+    epochs: list[int] = []
+    for latest_checkpoint in latest_checkpoints:
+        epochs.append(int(latest_checkpoint[len("checkpoint_epoch=") : -len(".pt")]))
+
+    epochs.sort()
+    final_epoch: int = epochs[-1]
+    monai_last_checkpoint: dict = torch.load(
+        f"{bundle_root_folder}/models/fold_{fold}/checkpoint_epoch={final_epoch}.pt"
+    )
+
+    best_checkpoints: list[str] = subfiles(
+        Path(bundle_root_folder).joinpath("models", f"fold_{fold}"), prefix="checkpoint_key_metric", sort=True
+    )
+    key_metrics: list[str] = []
+    for best_checkpoint in best_checkpoints:
+        key_metrics.append(str(best_checkpoint[len("checkpoint_key_metric=") : -len(".pt")]))
+
+    key_metrics.sort()
+    best_key_metric: str = key_metrics[-1]
+    monai_best_checkpoint: dict = torch.load(
+        f"{bundle_root_folder}/models/fold_{fold}/checkpoint_key_metric={best_key_metric}.pt"
+    )
+
+    nnunet_checkpoint["optimizer_state"] = monai_last_checkpoint["optimizer_state"]
+
+    nnunet_checkpoint["network_weights"] = odict()
+
+    for key in monai_last_checkpoint["network_weights"]:
+        nnunet_checkpoint["network_weights"][key] = monai_last_checkpoint["network_weights"][key]
+
+    nnunet_checkpoint["current_epoch"] = final_epoch
+    nnunet_checkpoint["logging"] = nnUNetLogger().get_checkpoint()
+    nnunet_checkpoint["_best_ema"] = 0
+    nnunet_checkpoint["grad_scaler_state"] = None
+
+    torch.save(nnunet_checkpoint, Path(nnunet_model_folder).joinpath(f"fold_{fold}", "checkpoint_final.pth"))
+
+    nnunet_checkpoint["network_weights"] = odict()
+
+    nnunet_checkpoint["optimizer_state"] = monai_best_checkpoint["optimizer_state"]
+
+    for key in monai_best_checkpoint["network_weights"]:
+        nnunet_checkpoint["network_weights"][key] = monai_best_checkpoint["network_weights"][key]
+
+    torch.save(nnunet_checkpoint, Path(nnunet_model_folder).joinpath(f"fold_{fold}", "checkpoint_best.pth"))
+
+    if not os.path.exists(os.path.join(nnunet_model_folder, "dataset.json")):
+        shutil.copy(f"{bundle_root_folder}/models/dataset.json", nnunet_model_folder)
+    if not os.path.exists(os.path.join(nnunet_model_folder, "plans.json")):
+        shutil.copy(f"{bundle_root_folder}/models/plans.json", nnunet_model_folder)
+    if not os.path.exists(os.path.join(nnunet_model_folder, "dataset_fingerprint.json")):
+        shutil.copy(f"{nnunet_preprocess_model_folder}/dataset_fingerprint.json", nnunet_model_folder)
+    if not os.path.exists(os.path.join(nnunet_model_folder, "nnunet_checkpoint.pth")):
+        shutil.copy(f"{bundle_root_folder}/models/nnunet_checkpoint.pth", nnunet_model_folder)