Towards Automatic Abdominal MRI Organ Segmentation: Leveraging Synthesized Data Generated From CT Labels
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arXiv
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| Auteurs principaux: | , , , , , |
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| Format: | Preprint |
| Publié: |
2024
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| _version_ | 1866929286547505152 |
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| author | Ciausu, Cosmin Krishnaswamy, Deepa Billot, Benjamin Pieper, Steve Kikinis, Ron Fedorov, Andrey |
| author_facet | Ciausu, Cosmin Krishnaswamy, Deepa Billot, Benjamin Pieper, Steve Kikinis, Ron Fedorov, Andrey |
| contents | Deep learning has shown great promise in the ability to automatically annotate organs in magnetic resonance imaging (MRI) scans, for example, of the brain. However, despite advancements in the field, the ability to accurately segment abdominal organs remains difficult across MR. In part, this may be explained by the much greater variability in image appearance and severely limited availability of training labels. The inherent nature of computed tomography (CT) scans makes it easier to annotate, resulting in a larger availability of expert annotations for the latter. We leverage a modality-agnostic domain randomization approach, utilizing CT label maps to generate synthetic images on-the-fly during training, further used to train a U-Net segmentation network for abdominal organs segmentation. Our approach shows comparable results compared to fully-supervised segmentation methods trained on MR data. Our method results in Dice scores of 0.90 (0.08) and 0.91 (0.08) for the right and left kidney respectively, compared to a pretrained nnU-Net model yielding 0.87 (0.20) and 0.91 (0.03). We will make our code publicly available. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_15609 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Towards Automatic Abdominal MRI Organ Segmentation: Leveraging Synthesized Data Generated From CT Labels Ciausu, Cosmin Krishnaswamy, Deepa Billot, Benjamin Pieper, Steve Kikinis, Ron Fedorov, Andrey Image and Video Processing Computer Vision and Pattern Recognition Deep learning has shown great promise in the ability to automatically annotate organs in magnetic resonance imaging (MRI) scans, for example, of the brain. However, despite advancements in the field, the ability to accurately segment abdominal organs remains difficult across MR. In part, this may be explained by the much greater variability in image appearance and severely limited availability of training labels. The inherent nature of computed tomography (CT) scans makes it easier to annotate, resulting in a larger availability of expert annotations for the latter. We leverage a modality-agnostic domain randomization approach, utilizing CT label maps to generate synthetic images on-the-fly during training, further used to train a U-Net segmentation network for abdominal organs segmentation. Our approach shows comparable results compared to fully-supervised segmentation methods trained on MR data. Our method results in Dice scores of 0.90 (0.08) and 0.91 (0.08) for the right and left kidney respectively, compared to a pretrained nnU-Net model yielding 0.87 (0.20) and 0.91 (0.03). We will make our code publicly available. |
| title | Towards Automatic Abdominal MRI Organ Segmentation: Leveraging Synthesized Data Generated From CT Labels |
| topic | Image and Video Processing Computer Vision and Pattern Recognition |
| url | https://arxiv.org/abs/2403.15609 |