Guided Synthesis of Labeled Brain MRI Data Using Latent Diffusion Models for Segmentation of Enlarged Ventricles
Fuente:
arXiv
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866909376150765568 |
|---|---|
| author | Ruschke, Tim Carlsen, Jonathan Frederik Hansen, Adam Espe Lindberg, Ulrich Hindsholm, Amalie Monberg Norgaard, Martin Ladefoged, Claes Nøhr |
| author_facet | Ruschke, Tim Carlsen, Jonathan Frederik Hansen, Adam Espe Lindberg, Ulrich Hindsholm, Amalie Monberg Norgaard, Martin Ladefoged, Claes Nøhr |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2411_01351 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Guided Synthesis of Labeled Brain MRI Data Using Latent Diffusion Models for Segmentation of Enlarged Ventricles Ruschke, Tim Carlsen, Jonathan Frederik Hansen, Adam Espe Lindberg, Ulrich Hindsholm, Amalie Monberg Norgaard, Martin Ladefoged, Claes Nøhr Computer Vision and Pattern Recognition Artificial Intelligence 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. |
| title | Guided Synthesis of Labeled Brain MRI Data Using Latent Diffusion Models for Segmentation of Enlarged Ventricles |
| topic | Computer Vision and Pattern Recognition Artificial Intelligence |
| url | https://arxiv.org/abs/2411.01351 |