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Changing the Contrast of Magnetic Resonance Imaging Signals using Deep Learning
Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.ORCID-id: 0000-0001-7119-7646
Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.ORCID-id: 0000-0002-0532-232X
Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Radiofysik.
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2021 (Engelska)Ingår i: Proceedings of the Fourth Conference on Medical Imaging with Deep Learning, PMLR / [ed] Mattias Heinrich; Qi Dou; Marleen de Bruijne; Jan Lellmann; Alexander Schläfer; Floris Ernst, Lübeck University; Hamburg University of Technology , 2021, Vol. 143, s. 713-727Konferensbidrag, Publicerat paper (Refereegranskat)
Abstract [en]

 The contrast settings to select before acquiring magnetic resonance imaging (MRI) signal depend heavily on the subsequent tasks. As each contrast highlights different tissues, automated segmentation tools for example might be optimized for a certain contrast. While for radiotherapy, multiple scans of the same region with different contrasts can achieve a better accuracy for delineating tumours and organs at risk. Unfortunately, the optimal contrast for the subsequent automated methods might not be known during the time of signal acquisition, and performing multiple scans with different contrasts increases the total examination time and registering the sequences introduces extra work and potential errors. Building on the recent achievements of deep learning in medical applications, the presented work describes a novel approach for transferring any contrast to any other. The novel model architecture incorporates the signal equation for spin echo sequences, and hence the model inherently learns the unknown quantitative maps for proton density, 𝑇1 and 𝑇2 relaxation times (𝑃𝐷, 𝑇1 and 𝑇2, respectively). This grants the model the ability to retrospectively reconstruct spin echo sequences by changing the contrast settings Echo and Repetition Time (𝑇𝐸 and 𝑇𝑅, respectively). The model learns to identify the contrast of pelvic MR images, therefore no paired data of the same anatomy from different contrasts is required for training. This means that the experiments are easily reproducible with other contrasts or other patient anatomies. Despite the contrast of the input image, the model achieves accurate results for reconstructing signal with contrasts available for evaluation. For the same anatomy, the quantitative maps are consistent for a range of contrasts of input images. Realized in practice, the proposed method would greatly simplify the modern radiotherapy pipeline. The trained model is made public together with a tool for testing the model on example images. 

Ort, förlag, år, upplaga, sidor
Lübeck University; Hamburg University of Technology , 2021. Vol. 143, s. 713-727
Serie
Proceedings of Machine Learning Research, ISSN 2640-3498
Nationell ämneskategori
Radiologi och bildbehandling Datorgrafik och datorseende
Identifikatorer
URN: urn:nbn:se:umu:diva-190497Scopus ID: 2-s2.0-85162848187OAI: oai:DiVA.org:umu-190497DiVA, id: diva2:1620813
Konferens
Medical Imaging with Deep Learning (MIDL), Online, 7-9 July, 2021.
Tillgänglig från: 2021-12-16 Skapad: 2021-12-16 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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