metadata

tags:
  - monai
  - medical
library_name: monai
license: apache-2.0

Model Overview

A pre-trained model for volumetric (3D) segmentation of brain tumor subregions from multimodal MRIs based on BraTS 2018 data. The whole pipeline is modified from clara_pt_brain_mri_segmentation.

The model is trained to segment 3 nested subregions of primary brain tumors (gliomas): the "enhancing tumor" (ET), the "tumor core" (TC), the "whole tumor" (WT) based on 4 aligned input MRI scans (T1c, T1, T2, FLAIR).

The ET is described by areas that show hyper intensity in T1c when compared to T1, but also when compared to "healthy" white matter in T1c.
The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and the non-enhancing (solid) parts of the tumor.
The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edema (ED), which is typically depicted by hyper-intense signal in FLAIR.

Data

The training data is from the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2018.

Target: 3 tumor subregions
Task: Segmentation
Modality: MRI
Size: 285 3D volumes (4 channels each)

The provided labelled data was partitioned, based on our own split, into training (200 studies), validation (42 studies) and testing (43 studies) datasets.

Preprocessing

The data list/split can be created with the script scripts/prepare_datalist.py.

python scripts/prepare_datalist.py --path your-brats18-dataset-path

Training configuration

This model utilized a similar approach described in 3D MRI brain tumor segmentation using autoencoder regularization, which was a winning method in BraTS2018 [1]. The training was performed with the following:

GPU: At least 16GB of GPU memory.
Actual Model Input: 224 x 224 x 144
AMP: True
Optimizer: Adam
Learning Rate: 1e-4
Loss: DiceLoss

Input

4 channel aligned MRIs at 1 x 1 x 1 mm

T1c
T1
T2
FLAIR

Output

3 channels

Label 0: TC tumor subregion
Label 1: WT tumor subregion
Label 2: ET tumor subregion

Performance

Dice score was used for evaluating the performance of the model. This model achieved Dice scores on the validation data of:

Tumor core (TC): 0.8559
Whole tumor (WT): 0.9026
Enhancing tumor (ET): 0.7905
Average: 0.8518

Please note that this bundle is non-deterministic because of the trilinear interpolation used in the network. Therefore, reproducing the training process may not get exactly the same performance. Please refer to https://pytorch.org/docs/stable/notes/randomness.html#reproducibility for more details about reproducibility.

Training Loss and Dice

Validation Dice

MONAI Bundle Commands

In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle. The CLI supports flexible use cases, such as overriding configs at runtime and predefining arguments in a file.

For more details usage instructions, visit the MONAI Bundle Configuration Page.

Execute training:

python -m monai.bundle run --config_file configs/train.json

Override the `train` config to execute multi-GPU training:

torchrun --standalone --nnodes=1 --nproc_per_node=8 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"

Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove --standalone, modify --nnodes, or do some other necessary changes according to the machine used. For more details, please refer to pytorch's official tutorial.

Override the `train` config to execute evaluation with the trained model:

python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"

Execute inference:

python -m monai.bundle run --config_file configs/inference.json

References

[1] Myronenko, Andriy. "3D MRI brain tumor segmentation using autoencoder regularization." International MICCAI Brainlesion Workshop. Springer, Cham, 2018. https://arxiv.org/abs/1810.11654.

License

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.