Auto-segmentation; carotid MRI; U-Net; uncertainty regularization; vessel segmentation; Auto segmentation; Biomedical imaging; Blood; Carotid artery; Carotid MRI; Regularisation; Three-dimensional display; U-net; Uncertainty; Uncertainty regularization; Vessel segmentation; Computer Science (all); Materials Science (all); Engineering (all); Electrical and Electronic Engineering; General Engineering; General Materials Science; General Computer Science
Abstract :
[en] We present a fully automated method for carotid artery (CA) outer wall segmentation in black blood MRI using partially annotated data and compare it to the state-of-the-art reference model. Our model was trained and tested on multicentric data of patients (106 and 23 patients, respectively) with a carotid plaque and was validated on different MR sequences (24 patients) as well as data that were acquired with MRI systems of a different vendor (34 patients). A 3D nnU-Net was trained on pre-contrast T1w turbo spin echo (TSE) MR images. A CA centerline sliding window approach was chosen to refine the nnU-Net segmentation using an additionally trained 2D U-Net to increase agreement with manual annotations. To improve segmentation performance in areas with semantically and visually challenging voxels, Monte-Carlo dropout was used. To increase generalizability, data were augmented with intensity transformations. Our method achieves state-of-the-art results yielding a Dice similarity coefficient (DSC) of 91.7% (interquartile range (IQR) 3.3%) and volumetric intraclass correlation (ICC) with ground truth of 0.90 on the development domain data and a DSC of 91.1% (IQR 7.2%) and volumetric ICC with ground truth of 0.83 on the external domain data outperforming top-ranked methods for open-source CA segmentation. The uncertainty-based approach increases the interpretability of the proposed method by providing an uncertainty map together with the segmentation.
Disciplines :
Computer science
Author, co-author :
Lavrova, Elizaveta ; Université de Liège - ULiège > GIGA ; GROW-School for Oncology and Reproduction, Maastricht University, D-Laboratory, Department of Precision Medicine, Maastricht, Netherlands
Salahuddin, Zohaib; GROW-School for Oncology and Reproduction, Maastricht University, D-Laboratory, Department of Precision Medicine, Maastricht, Netherlands
Woodruff, Henry C. ; GROW-School for Oncology and Reproduction, Maastricht University, D-Laboratory, Department of Precision Medicine, Maastricht, Netherlands ; Maastricht University Medical Centre+, Department of Radiology and Nuclear Medicine, Maastricht, Netherlands
Kassem, Mohamed; Maastricht University Medical Centre+, Department of Radiology and Nuclear Medicine, Maastricht, Netherlands ; Maastricht University, CARIM School for Cardiovascular Diseases, Maastricht, Netherlands
Camarasa, Robin; Erasmus University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Rotterdam, Netherlands
Van Kolk, Anja G. Der ; University Medical Center Utrecht, Department of Radiology, Utrecht, Netherlands ; Radboudumc, Department of Medical Imaging, Nijmegen, Netherlands
Nederkoorn, Paul J.; Amsterdam UMC, Department of Neurology, Amsterdam, Netherlands
Bos, Daniel; Erasmus University Medical Center Rotterdam, Department of Radiology and Nuclear Medicine, Rotterdam, Netherlands
Hendrikse, Jeroen; University Medical Center Utrecht, Department of Radiology, Utrecht, Netherlands
Kooi, M. Eline ; Maastricht University Medical Centre+, Department of Radiology and Nuclear Medicine, Maastricht, Netherlands ; Maastricht University, CARIM School for Cardiovascular Diseases, Maastricht, Netherlands
Lambin, Philippe; GROW-School for Oncology and Reproduction, Maastricht University, D-Laboratory, Department of Precision Medicine, Maastricht, Netherlands ; Maastricht University Medical Centre+, Department of Radiology and Nuclear Medicine, Maastricht, Netherlands
Language :
English
Title :
UR-CarA-Net: A Cascaded Framework with Uncertainty Regularization for Automated Segmentation of Carotid Arteries on Black Blood MR Images
Publication date :
2023
Journal title :
IEEE Access
ISSN :
2169-3536
Publisher :
Institute of Electrical and Electronics Engineers Inc.
H2020 - 952172 - CHAIMELEON - Accelerating the lab to market transition of AI tools for cancer management
Funders :
EU - European Union IMI - Innovative Medicines Initiative
Funding text :
This work was supported in part by the European Union’s Horizon 2020 Research and Innovation Program CHAIMELEON under Grant
952172, in part by EuCanImage under Grant 952103, in part by the TRANSCAN Joint Transnational Call 2016 (JTC2016 CLEARLY)
under Grant UM 2017-8295, and in part by the Innovative Medicines Initiative (IMI)-Optimal Treatment for Patients with Solid Tumours
in Europe Through Artificial intelligence (OPTIMA) under Grant 101034347. The work of Elizaveta Lavrova was supported by the
Liege-Maastricht Imaging Valley Grant.
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