Multi-class semantic segmentation

For the multi-class semantic segmentation task, we will use the brain tumors dataset from the Medical Segmentation Decathlon challenge (http://medicaldecathlon.com/). The data is collected from the Multimodal Brain Tumor Image Segmentation Benchmark Challenge (BraTS) dataset from 2016 and 2017. The task is to segment tumors into three different subregions (active tumor (AT), necrotic core (NCR), and peritumoral edematous/infiltrated tissue (ED)) from multimodal multisite MRI data (T1w, T1ce, T2w, and FLAIR). The challenge with this dataset is the brain tumors’ highly heterogeneous appearance and shape.

Google Colab
from fastMONAI.vision_all import *

from monai.apps import DecathlonDataset
from sklearn.model_selection import train_test_split

Download external data

We use the MONAI function DecathlonDataset to download the data and generate items for training.

path = Path('../data')
path.mkdir(exist_ok=True)
task = "Task01_BrainTumour"
training_data = DecathlonDataset(root_dir=path, task=task, section="training", download=True,
                                 cache_num=0, num_workers=3)
2025-08-29 09:44:58,814 - INFO - Verified 'Task01_BrainTumour.tar', md5: 240a19d752f0d9e9101544901065d872.
2025-08-29 09:44:58,815 - INFO - File exists: ../data/Task01_BrainTumour.tar, skipped downloading.
2025-08-29 09:44:58,816 - INFO - Non-empty folder exists in ../data/Task01_BrainTumour, skipped extracting.
df = pd.DataFrame(training_data.data)
df.shape
(388, 2)

Split the labled data into training and test

train_df, test_df = train_test_split(df, test_size=0.1, random_state=42)
train_df.shape, test_df.shape
((349, 2), (39, 2))

Look at training data

med_dataset = MedDataset(img_list=train_df.label.tolist(), dtype=MedMask, max_workers=12)
med_dataset.df.head()
path dim_0 dim_1 dim_2 voxel_0 voxel_1 voxel_2 orientation voxel_count_0 voxel_count_1 voxel_count_2 voxel_count_3
0 ../data/Task01_BrainTumour/labelsTr/BRATS_477.nii.gz 240 240 155 1.0 1.0 1.0 RAS+ 8765377 83088 15826 63709.0
1 ../data/Task01_BrainTumour/labelsTr/BRATS_350.nii.gz 240 240 155 1.0 1.0 1.0 RAS+ 8872636 21364 8872 25128.0
2 ../data/Task01_BrainTumour/labelsTr/BRATS_266.nii.gz 240 240 155 1.0 1.0 1.0 RAS+ 8725071 83276 69784 49869.0
3 ../data/Task01_BrainTumour/labelsTr/BRATS_294.nii.gz 240 240 155 1.0 1.0 1.0 RAS+ 8790699 90806 20231 26264.0
4 ../data/Task01_BrainTumour/labelsTr/BRATS_466.nii.gz 240 240 155 1.0 1.0 1.0 RAS+ 8911252 14046 60 2642.0
summary_df = med_dataset.summary()
summary_df.head()
dim_0 dim_1 dim_2 voxel_0 voxel_1 voxel_2 orientation example_path total
0 240 240 155 1.0 1.0 1.0 RAS+ ../data/Task01_BrainTumour/labelsTr/BRATS_002.nii.gz 349
resample, reorder = med_dataset.suggestion()
resample, reorder
([1.0, 1.0, 1.0], False)
img_size = med_dataset.get_largest_img_size(resample=resample)
img_size
[240.0, 240.0, 155.0]
bs=4
size=[224,224,128]
item_tfms = [ZNormalization(), PadOrCrop(size), RandomAffine(scales=0, degrees=5, isotropic=True)]
dblock = MedDataBlock(blocks=(ImageBlock(cls=MedImage), MedMaskBlock), 
                      splitter=RandomSplitter(seed=42),
                      get_x=ColReader('image'),
                      get_y=ColReader('label'),
                      item_tfms=item_tfms,
                      reorder=reorder,
                      resample=resample)
dls = dblock.dataloaders(train_df, bs=bs)
# training and validation
len(dls.train_ds.items), len(dls.valid_ds.items)
(280, 69)
dls.show_batch(anatomical_plane=0)

Create and train a 3D model

As in the binary segmentation task, we import an enhanced version of UNet from MONAI. This time instead of using Dice loss, we import a loss function that combines Dice loss and Cross Entropy loss and returns the weighted sum of these two losses.

from monai.losses import DiceCELoss
from monai.networks.nets import UNet
codes = np.unique(med_img_reader(train_df.label.tolist()[0]))
n_classes = len(codes)
print("Unique classes:",*codes)
Unique classes: 0.0 1.0 2.0 3.0
monai_model = UNet(spatial_dims=3, in_channels=4, out_channels=n_classes, channels=(16, 32, 64, 128, 256),strides=(2, 2, 2, 2), num_res_units=2)
pytorch_model = monai_model.model
loss_func = CustomLoss(loss_func=DiceCELoss(to_onehot_y=True, include_background=True, softmax=True))
learn = Learner(dls, monai_model, loss_func=loss_func, opt_func=ranger, metrics=multi_dice_score)#.to_fp16()
learn.lr_find()
SuggestedLRs(valley=0.001737800776027143)

lr = 1e-1
import mlflow

# Set experiment name
mlflow.set_experiment(task)

mlflow_callback = ModelTrackingCallback(
    model_name=f"{task}_{monai_model._get_name()}",
    loss_function=loss_func.loss_func._get_name(),
    item_tfms=item_tfms,
    size=size,
    resample=resample,
    reorder=reorder,
)

with mlflow.start_run(run_name="initial_training"):
    learn.fit_flat_cos(2, lr, cbs=[mlflow_callback])
learn.save('braintumor-weights')
Path('models/braintumor-model.pth')
learn.show_results(anatomical_plane=0, ds_idx=1)

mlflow_ui = MLflowUIManager()
mlflow_ui.start_ui()

Inference on test data

learn.load('braintumor-weights');
test_dl = learn.dls.test_dl(test_df[:10],with_labels=True)
test_dl.show_batch(anatomical_plane=0, figsize=(10,10))

pred_acts, labels = learn.get_preds(dl=test_dl)
pred_acts.shape, labels.shape
(torch.Size([10, 4, 224, 224, 128]), torch.Size([10, 1, 224, 224, 128]))

Dice score for labels 1,2 and 3:

multi_dice_score(pred_acts, labels)
tensor([0.5708, 0.4186, 0.6994])
learn.show_results(anatomical_plane=0, dl=test_dl)

mlflow_ui.stop()