Guided Synthesis of Labeled Brain MRI Data Using Latent Diffusion Models for Segmentation of Enlarged Ventricles

TL;DR

This paper introduces a novel method using latent diffusion models to generate labeled brain MRI data, which enhances ventricular segmentation accuracy and outperforms existing models, addressing data scarcity in medical imaging.

Contribution

The study presents a new guided synthesis approach with latent diffusion models for creating labeled MRI data, improving segmentation of enlarged ventricles.

Findings

Synthetic data trained models achieved lower MAE than real data models.

The synthetic data model outperformed the state-of-the-art SynthSeg in MAE and standard deviation.

Augmented data training yielded the highest Dice score, comparable to real data training.

Abstract

Deep learning models in medical contexts face challenges like data scarcity, inhomogeneity, and privacy concerns. This study focuses on improving ventricular segmentation in brain MRI images using synthetic data. We employed two latent diffusion models (LDMs): a mask generator trained using 10,000 masks, and a corresponding SPADE image generator optimized using 6,881 scans to create an MRI conditioned on a 3D brain mask. Conditioning the mask generator on ventricular volume in combination with classifier-free guidance enabled the control of the ventricular volume distribution of the generated synthetic images. Next, the performance of the synthetic data was tested using three nnU-Net segmentation models trained on a real, augmented and entirely synthetic data, respectively. The resulting models were tested on a completely independent hold-out dataset of patients with enlarged ventricles, with manual delineation of the ventricles used as ground truth. The model trained on real data showed a mean absolute error (MAE) of 9.09 \pm 12.18 mL in predicted ventricular volume, while the models trained on synthetic and augmented data showed MAEs of 7.52 \pm 4.81 mL and 6.23 \pm 4.33 mL, respectively. Both the synthetic and augmented model also outperformed the state-of-the-art model SynthSeg, which due to limited performance in cases of large ventricular volumes, showed an MAE of 7.73 \pm 12.12 mL with a factor of 3 higher standard deviation. The model trained on augmented data showed the highest Dice score of 0.892 \pm 0.05, slightly outperforming SynthSeg and on par with the model trained on real data. The synthetic model performed similar to SynthSeg. In summary, we provide evidence that guided synthesis of labeled brain MRI data using LDMs improves the segmentation of enlarged ventricles and outperforms existing state-of-the-art segmentation models.