app.py

import gradio as gr
import torch
import numpy as np
import pandas as pd
import os
import torchio
import torch.nn as nn
from huggingface_hub import hf_hub_download
from monai.transforms import Compose, LoadImaged, Spacingd, CropForegroundd, SpatialPadd, CenterSpatialCropd
from monai.data import Dataset
from nnunet_mednext import create_mednext_encoder_v1

# Debugging GPU environment
if torch.cuda.is_available():
    print(f"GPU is available: {torch.cuda.get_device_name(0)}")
else:
    print("No GPU available. Falling back to CPU.")
    os.system("nvidia-smi")

# Device selection
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

# Model definition
class MedNeXtEncReg(nn.Module):
    def __init__(self):
        super(MedNeXtEncReg, self).__init__()
        self.mednextv1 = create_mednext_encoder_v1(
            num_input_channels=1, num_classes=1, model_id='B', kernel_size=3, deep_supervision=True
        )
        self.global_avg_pool = nn.AdaptiveAvgPool3d((1, 1, 1))
        self.regression_fc = nn.Sequential(
            nn.Linear(512, 64),
            nn.ReLU(),
            nn.Dropout(0.0),
            nn.Linear(64, 1)
        )

    def forward(self, x):
        x = self.mednextv1(x)
        x = self.global_avg_pool(x)
        x = torch.flatten(x, start_dim=1)
        age_estimate = self.regression_fc(x)
        return age_estimate.squeeze()

# Download the model from Hugging Face Hub
def initialize_model():
    model_paths = [
        hf_hub_download(repo_id="FrancescoLR/BrainAgeNeXt", filename=f"BrainAge_{i}.pth") for i in range(1, 6)
    ]
    
    models = []
    for model_path in model_paths:
        model = MedNeXtEncReg().to(device)
        model.load_state_dict(torch.load(model_path, map_location=device))
        model.eval()
        models.append(model)
    return models

# Define preprocessing transforms
def prepare_transforms():
    return Compose([
        LoadImaged(keys=["image"], ensure_channel_first=True),
        Spacingd(keys=["image"], pixdim=(1.0, 1.0, 1.0)),
        CropForegroundd(keys=["image"], allow_smaller=True, source_key="image"),
        SpatialPadd(keys=["image"], spatial_size=(160, 192, 160)),
        CenterSpatialCropd(keys=["image"], roi_size=(160, 192, 160)),
        torchio.transforms.ZNormalization(masking_method=lambda x: x > 0, keys=["image"])
    ])

# Process uploaded MRI scan
def preprocess_mri(mri_path):
    transforms = prepare_transforms()
    data_dict = {"image": mri_path}
    dataset = Dataset([data_dict], transform=transforms)
    dataloader = DataLoader(dataset, batch_size=1, num_workers=0)
    return next(iter(dataloader))["image"].to(device)

# Predict brain age
def predict_brain_age(mri_path, actual_age, sex):
    if not os.path.exists(mri_path):
        return "Error: MRI file not found"

    # Load the model
    models = initialize_model()

    # Preprocess MRI
    image = preprocess_mri(mri_path)

    # Run predictions
    predictions = []
    with torch.no_grad():
        for model in models:
            pred = model(image)
            predictions.append(pred.cpu().numpy())

    # Compute median brain age prediction
    predicted_brain_age = np.median(np.stack(predictions))

    # Apply correction based on actual age
    predicted_brain_age_corrected = (
        predicted_brain_age + (actual_age * 0.062) - 2.96 if actual_age > 18 else predicted_brain_age
    )

    brain_age_difference = predicted_brain_age_corrected - actual_age

    # Output results
    return f"Predicted Brain Age: {predicted_brain_age_corrected:.2f} years", \
           f"Brain Age Difference (BAD): {brain_age_difference:.2f} years"

# Gradio UI
demo = gr.Interface(
    fn=predict_brain_age,
    inputs=[
        gr.File(label="Upload MRI (NIfTI .nii.gz)"),
        gr.Number(label="Enter Age"),
        gr.Radio(["Male", "Female"], label="Select Sex")
    ],
    outputs=[
        gr.Textbox(label="Predicted Brain Age"),
        gr.Textbox(label="Brain Age Difference (BAD)")
    ],
    title="Brain Age Prediction with MedNeXt",
    description="Upload an MRI scan (.nii.gz), enter your age and sex, and get a brain age prediction.",
    theme="default"
)

# Launch the Gradio app
if __name__ == "__main__":
    demo.launch(share=True)