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3D-EPI Blip-Up/Down Acquisition (BUDA) with CAIPI and Joint Hankel Structured Low-Rank Reconstruction for Rapid Distortion-Free High-Resolution T2* Mapping

arXiv

引用

arXiv 2022年

作者： Chen, Zhifeng Liao, Congyu Cao, Xiaozhi Poser, Benedikt A. Xu, Zhongbiao Lo, Wei-Ching Wen, Manyi Cho, Jaejin Tian, Qiyuan Wang, Yaohui Feng, Yanqiu Xia, Ling Chen, Wufan Liu, Feng Bilgic, Berkin School of Biomedical Engineering Guangdong Provincial Key Laboratory of Medical Image Processing Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology Southern Medical University Guangzhou China Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital CharlestownMA United States Department of Radiology Harvard Medical School CharlestownMA United States Department of Data Science and AI Faculty of IT Monash University ClaytonVIC Australia Department of Radiology Stanford University Stanford CA United States Maastricht Brain Imaging Center Faculty of Psychology and Neuroscience University of Maastricht Netherlands Department of Radiotherapy Cancer Center Guangdong Provincial People's Hospital Guangdong Academy of Medical Science Guangzhou China Siemens Medical Solutions BostonMA United States Department of Chemical Pathology The Chinese University of Hong Kong Hong Kong Division of Superconducting Magnet Science and Technology Institute of Electrical Engineering Chinese Academy of Sciences Beijing China Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence Key Laboratory of Mental Health of the Ministry of Education Southern Medical University Guangzhou China Department of Biomedical Engineering Zhejiang University Hangzhou China Research Center for Healthcare Data Science Zhejiang Lab Hangzhou China School of Information Technology and Electrical Engineering The University of Queensland BrisbaneQLD Australia Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States

Purpose: This work aims to develop a novel distortion-free 3D-EPI acquisition and image reconstruction technique for fast and robust, high-resolution, whole-brain imaging as well as quantitative T2* mapping. Methods: 3D-Blip-Up and -Down Acquisition (3D-BUDA) sequence is designed for both single- and multi-echo 3D GRE-EPI imaging using multiple shots with blip-up and -down readouts to encode B0 field map information. Complementary k-space coverage is achieved using controlled aliasing in parallel imaging (CAIPI) sampling across the shots. For image reconstruction, an iterative hard-thresholding algorithm is employed to minimize the cost function that combines field map information informed parallel imaging with the structured low-rank constraint for multi-shot 3D-BUDA data. Extending 3D-BUDA to multi-echo imaging permits T2* mapping. For this, we propose constructing a joint Hankel matrix along both echo and shot dimensions to improve the reconstruction. Results: Experimental results on in vivo multi-echo data demonstrate that, by performing joint reconstruction along with both echo and shot dimensions, reconstruction accuracy is improved compared to standard 3D-BUDA reconstruction. CAIPI sampling is further shown to enhance the image quality. For T2* mapping, T2* values from 3D-Joint-CAIPI-BUDA and reference multi-echo GRE are within limits of agreement as quantified by Bland-Altman analysis. Conclusions: The proposed technique enables rapid 3D distortion-free high-resolution imaging and T2* mapping. Specifically, 3D-BUDA enables 1-mm isotropic whole-brain imaging in 22 s at 3 T and 9 s on a 7 T scanner. The combination of multi-echo 3D-BUDA with CAIPI acquisition and joint reconstruction enables distortion-free whole-brain T2* mapping in 47 s at 1.1×1.1×1.0 mm3 resolution. Copyright © 2022, The Authors. All rights reserved.

关键词： Mapping

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Fetal Brain Tissue Annotation and Segmentation Challenge Results

arXiv

引用

arXiv 2022年

作者： Payette, Kelly Li, Hongwei De Dumast, Priscille Licandro, Roxane Ji, Hui Siddiquee, Md Mahfuzur Rahman Xu, Daguang Myronenko, Andriy Liu, Hao Pei, Yuchen Wang, Lisheng Peng, Ying Xie, Juanying Zhang, Huiquan Dong, Guiming Fu, Hao Wang, Guotai Rieu, ZunHyan Kim, Donghyeon Kim, Hyun Gi Karimi, Davood Gholipour, Ali Torres, Helena R. Oliveira, Bruno Vilaça, João L. Lin, Yang Avisdris, Netanell Ben-Zvi, Ori Bashat, Dafna Ben Fidon, Lucas Aertsen, Michael Vercauteren, Tom Sobotka, Daniel Langs, Georg Alenyà, Mireia Villanueva, Maria Inmaculada Camara, Oscar Fadida, Bella Specktor Joskowicz, Leo Weibin, Liao Yi, Lv Xuesong, Li Mazher, Moona Qayyum, Abdul Puig, Domenec Kebiri, Hamza Zhang, Zelin Xu, Xinyi Wu, Dan Liao, KuanLun Wu, YiXuan Chen, JinTai Xu, Yunzhi Zhao, Li Vasung, Lana Menze, Bjoern Cuadra, Meritxell Bach Jakab, Andras Center for MR Research University Children's Hospital Zurich University of Zurich Zurich Switzerland Neuroscience Center Zurich University of Zurich Zurich Switzerland Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Informatics Technical University of Munich Munich Germany Medical Image Analysis Laboratory Department of Diagnostic and Interventional Radiology Lausanne University Hospital University of Lausanne Lausanne Switzerland CIBM Center for Biomedical Imaging Lausanne Switzerland Laboratory for Computational Neuroimaging Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School CharlestownMA United States Medical University of Vienna Vienna Austria Arizona State University United States NVIDIA United States Shanghai Jiaotong University China School of Computer Science Shaanxi Normal University Xi'An710119 China Research Institute NEUROPHET Inc. Seoul06247 Korea Republic of Department of Radiology The Catholic University of Korea Eunpyeong St. Mary's Hospital Seoul06247 Korea Republic of Boston Children's Hospital Harvard Medical School BostonMA United States 2Ai - School of Technology IPCA Barcelos Portugal Algoritmi Center School of Engineering University of Minho Guimarães Portugal School of Medicine University of Minho Braga Portugal ICVS 3B's - PT Government Associate Laboratory Guimarães Braga Portugal School of Computer Science and Engineering The Hebrew University of Jerusalem Israel Sagol Brain Institute Tel Aviv Sourasky Medical Center Israel Sagol School of Neuroscience Tel Aviv University Israel Sackler Faculty of Medicine Tel Aviv University Israel School of Biomedical Engineering & Imaging Sciences King's College London LondonSE1 7EU United Kingdom Department of Radiology University Hospitals Leuven Leuven3000 Belgium Computational Imaging Research Lab Department of Biomedical Imaging and Image-guided Therapy Medical

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero. © 2022, CC BY.

关键词： Magnetic resonance imaging

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QUBIQ: Uncertainty Quantification for Biomedical image Segmentation Challenge

arXiv

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arXiv 2024年

作者： Li, Hongwei Bran Navarro, Fernando Ezhov, Ivan Bayat, Amirhossein Das, Dhritiman Kofler, Florian Shit, Suprosanna Waldmannstetter, Diana Paetzold, Johannes C. Hu, Xiaobin Wiestler, Benedikt Zimmer, Lucas Amiranashvili, Tamaz Prabhakar, Chinmay Berger, Christoph Weidner, Jonas Alonso-Basanta, Michelle Rashid, Arif Baid, Ujjwal Adel, Wesam Alis, Deniz Baheti, Bhakti Bai, Yingbin Bhat, Ishaan Cetindag, Sabri Can Chen, Wenting Cheng, Li Dutande, Prasad Dular, Lara Elattar, Mustafa A. Feng, Ming Gao, Shengbo Huisman, Henkjan Hu, Weifeng Innani, Shubham Ji, Wei Karimi, Davood Kuijf, Hugo J. Kwak, Jin Tae Le, Hoang Long Li, Xiang Lin, Huiyan Liu, Tongliang Ma, Jun Ma, Kai Ma, Ting Oksuz, Ilkay Holland, Robbie Oliveira, Arlindo L. Pal, Jimut Bahan Pei, Xuan Qiao, Maoying Saha, Anindo Selvan, Raghavendra Shen, Linlin Silva, Joao Lourenco Spiclin, Ziga Talbar, Sanjay Wang, Dadong Wang, Wei Wang, Xiong Wang, Yin Xi, Ruiling Xu, Kele Yang, Yanwu Yergin, Mert Yu, Shuang Zeng, Lingxi Zhang, YingLin Zhao, Jiachen Zheng, Yefeng Zukovec, Martin Do, Richard Becker, Anton Simpson, Amber Konukoglu, Ender Jakab, Andras Bakas, Spyridon Joskowicz, Leo Menze, Bjoern Department of Informatics Technical University of Munich Germany Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School United States Department of Quantitative Biomedicine University of Zurich Switzerland University Children’s Hospital Zurich University of Zurich Switzerland Department of Radioncology and Radiation Theraphy Klinikum rechts der Isar Technical University of Munich Germany Department of Information Technology and Electrical Engineering ETH-Zurich Switzerland Department of Radiology Memorial Sloan Kettering Cancer Center New York City United States Department of Biomedical and Molecular Sciences Queen’s University Canada TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany McGovern Institute Massachusetts Institute of Technology United States Institute for Diagnostic and Interventional Radiology Unveristy Zurich Hospital Switzerland BioMedIA Imperial College London United Kingdom Department of Radiation Oncology University of Pennsylvania PA United States University of Pennsylvania PA United States Department of Radiation Oncology Winship Cancer Institute of Emory University Georgia United States Nile University Cairo Egypt Department of Medical Sciences Acibadem University Istanbul Turkey Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Trustworthy Machine Learning Lab University of Sydney Australia Image Sciences Institute University Medical Center Utrecht Netherlands Computer Engineering Department Istanbul Technical University Istanbul Turkey School of Computer Science Shenzhen University Shenzhen China University of Alberta United States University of Ljubljana Faculty of Electrical Engineering Ljubljana Slovenia Tongji University Shanghai China OPPO Research Institute Shanghai China School of Biological and Medical Engineering Beihang University Beijing China Harvard Medical School Boston

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT;various organs such as the brain, prostate, kidney, and pancreas;and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks. © 2024, CC BY-NC-ND.

关键词： image segmentation

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