MRI brain tumor segmentation and uncertainty estimation using 3D-UNet architectures
Automation of brain tumor segmentation in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. M...
| Autores: | , |
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| Tipo de documento: | capítulo de livro |
| Data de publicação: | 2021 |
| País: | España |
| Recursos: | Universitat Politècnica de Catalunya (UPC) |
| Repositório: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglês |
| OAI Identifier: | oai:upcommons.upc.edu:2117/360072 |
| Acesso em linha: | https://hdl.handle.net/2117/360072 https://dx.doi.org/10.1007/978-3-030-72084-1_34 |
| Access Level: | Acceso aberto |
| Palavra-chave: | Brain -- Magnetic resonance imaging Brain -- Tumors -- Diagnosis Brain tumor segmentation Deep learning Uncertainty 3d convolutional neural networks Cervell -- Imatgeria per ressonància magnètica Cervell -- Tumors -- Diagnòstic Àrees temàtiques de la UPC::Enginyeria de la telecomunicació::Processament del senyal::Processament de la imatge i del senyal vídeo |
| Resumo: | Automation of brain tumor segmentation in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high memory consumption is still a problem in 3D-CNNs. Moreover, most methods do not include uncertainty information, which is especially critical in medical diagnosis. This work studies 3D encoder-decoder architectures trained with patch-based techniques to reduce memory consumption and decrease the effect of unbalanced data. The different trained models are then used to create an ensemble that leverages the properties of each model, thus increasing the performance. We also introduce voxel-wise uncertainty information, both epistemic and aleatoric using test-time dropout (TTD) and data-augmentation (TTA) respectively. In addition, a hybrid approach is proposed that helps increase the accuracy of the segmentation. The model and uncertainty estimation measurements proposed in this work have been used in the BraTS’20 Challenge for task 1 and 3 regarding tumor segmentation and uncertainty estimation. |
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