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MRI bias field correction with an implicitly trained CNN
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
Umeå University, Faculty of Science and Technology, Department of Computing Science. (Machine Learning)ORCID iD: 0000-0001-7119-7646
Umeå University, Faculty of Medicine, Department of Radiation Sciences.ORCID iD: 0000-0002-0532-232X
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.ORCID iD: 0000-0002-8971-9788
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2022 (English)In: Proceedings of the 5th international conference on medical imaging with deep learning / [ed] Ender Konukoglu; Bjoern Menze; Archana Venkataraman; Christian Baumgartner; Qi Dou; Shadi Albarqouni, ML Research Press , 2022, p. 1125-1138Conference paper, Published paper (Refereed)
Abstract [en]

In magnetic resonance imaging (MRI), bias fields are difficult to correct since they are inherently unknown. They cause intra-volume intensity inhomogeneities which limit the performance of subsequent automatic medical imaging tasks, \eg, tissue-based segmentation. Since the ground truth is unavailable, training a supervised machine learning solution requires approximating the bias fields, which limits the resulting method. We introduce implicit training which sidesteps the inherent lack of data and allows the training of machine learning solutions without ground truth. We describe how training a model implicitly for bias field correction allows using non-medical data for training, achieving a highly generalized model. The implicit approach was compared to a more traditional training based on medical data. Both models were compared to an optimized N4ITK method, with evaluations on six datasets. The implicitly trained model improved the homogeneity of all encountered medical data, and it generalized better for a range of anatomies, than the model trained traditionally. The model achieves a significant speed-up over an optimized N4ITK method—by a factor of 100, and after training, it also requires no parameters to tune. For tasks such as bias field correction - where ground truth is generally not available, but the characteristics of the corruption are known - implicit training promises to be a fruitful alternative for highly generalized solutions.

Place, publisher, year, edition, pages
ML Research Press , 2022. p. 1125-1138
Series
Proceedings of Machine Learning Research, ISSN 2640-3498 ; 172
Keywords [en]
Self-supervised learning, Implicit Training, Magnetic Resonance Imaging, Bias Field Correction, Image Restoration
National Category
Radiology, Nuclear Medicine and Medical Imaging Computer graphics and computer vision
Identifiers
URN: urn:nbn:se:umu:diva-205226Scopus ID: 2-s2.0-85169103625OAI: oai:DiVA.org:umu-205226DiVA, id: diva2:1739650
Conference
International Conference on Medical Imaging with Deep Learning, Zurich, Switzerland, July 6-8, 2022
Available from: 2023-02-27 Created: 2023-02-27 Last updated: 2025-02-01Bibliographically approved
In thesis
1. Contributions to deep learning for imaging in radiotherapy
Open this publication in new window or tab >>Contributions to deep learning for imaging in radiotherapy
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Bidrag till djupinlärning för bildbehandling inom strålbehandling
Abstract [en]

Purpose: The increasing importance of medical imaging in cancer treatment, combined with the growing popularity of deep learning gave relevance to the presented contributions to deep learning solutions with applications in medical imaging.

Relevance: The projects aim to improve the efficiency of MRI for automated tasks related to radiotherapy, building on recent advancements in the field of deep learning.

Approach: Our implementations are built on recently developed deep learning methodologies, while introducing novel approaches in the main aspects of deep learning, with regards to physics-informed augmentations and network architectures, and implicit loss functions. To make future comparisons easier, we often evaluated our methods on public datasets, and made all solutions publicly available.

Results: The results of the collected projects include the development of robust models for MRI bias field correction, artefact removal, contrast transfer and sCT generation. Furthermore, the projects stress the importance of reproducibility in deep learning research and offer guidelines for creating transparent and usable code repositories.

Conclusions: Our results collectively build the position of deep learning in the field of medical imaging. The projects offer solutions that are both novel and aim to be highly applicable, while emphasizing generalization towards a wide variety of data and the transparency of the results.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2023. p. 100
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 2264
Keywords
deep learning, medical imaging, radiotherapy, artefact correction, bias field correction, contrast transfer, synthetic CT, reproducibility
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-215693 (URN)9789180701945 (ISBN)9789180701952 (ISBN)
Public defence
2024-01-26, E04, Norrlands universitetssjukhus, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2023-11-08 Created: 2023-10-25 Last updated: 2024-07-02Bibliographically approved

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Simkó, AttilaLöfstedt, TommyGarpebring, AndersNyholm, TufveJonsson, Joakim

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Radiation PhysicsDepartment of Computing ScienceDepartment of Radiation Sciences
Radiology, Nuclear Medicine and Medical ImagingComputer graphics and computer vision

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