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MRI bias field correction with an implicitly trained CNN
Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. (Machine Learning)ORCID-id: 0000-0001-7119-7646
Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper.ORCID-id: 0000-0002-0532-232X
Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.ORCID-id: 0000-0002-8971-9788
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2022 (Engelska)Ingår i: 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, s. 1125-1138Konferensbidrag, Publicerat paper (Refereegranskat)
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.

Ort, förlag, år, upplaga, sidor
ML Research Press , 2022. s. 1125-1138
Serie
Proceedings of Machine Learning Research, ISSN 2640-3498 ; 172
Nyckelord [en]
Self-supervised learning, Implicit Training, Magnetic Resonance Imaging, Bias Field Correction, Image Restoration
Nationell ämneskategori
Radiologi och bildbehandling Datorgrafik och datorseende
Identifikatorer
URN: urn:nbn:se:umu:diva-205226Scopus ID: 2-s2.0-85169103625OAI: oai:DiVA.org:umu-205226DiVA, id: diva2:1739650
Konferens
International Conference on Medical Imaging with Deep Learning, Zurich, Switzerland, July 6-8, 2022
Tillgänglig från: 2023-02-27 Skapad: 2023-02-27 Senast uppdaterad: 2025-02-01Bibliografiskt granskad
Ingår i avhandling
1. Contributions to deep learning for imaging in radiotherapy
Öppna denna publikation i ny flik eller fönster >>Contributions to deep learning for imaging in radiotherapy
2023 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Alternativ titel[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.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå University, 2023. s. 100
Serie
Umeå University medical dissertations, ISSN 0346-6612 ; 2264
Nyckelord
deep learning, medical imaging, radiotherapy, artefact correction, bias field correction, contrast transfer, synthetic CT, reproducibility
Nationell ämneskategori
Radiologi och bildbehandling
Identifikatorer
urn:nbn:se:umu:diva-215693 (URN)9789180701945 (ISBN)9789180701952 (ISBN)
Disputation
2024-01-26, E04, Norrlands universitetssjukhus, Umeå, 13:00 (Engelska)
Opponent
Handledare
Tillgänglig från: 2023-11-08 Skapad: 2023-10-25 Senast uppdaterad: 2024-07-02Bibliografiskt granskad

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Simkó, AttilaLöfstedt, TommyGarpebring, AndersNyholm, TufveJonsson, Joakim

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Simkó, AttilaLöfstedt, TommyGarpebring, AndersNyholm, TufveJonsson, Joakim
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RadiofysikInstitutionen för datavetenskapInstitutionen för strålningsvetenskaper
Radiologi och bildbehandlingDatorgrafik och datorseende

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