Uncertainty-Aware Cortical Surface Reconstruction and Spherical Registration for Heterogeneous Brain MRI
Danish Research Centre for Magnetic Resonance, Department of Radiology and Nuclear Medicine, Copenhagen University Hospital – Amager and Hvidovre（丹麦磁共振研究中心，放射科与核医学科，哥本哈根大学医院-阿马格和维多弗）；Department of Health Technology, Technical University of Denmark（技术丹麦大学健康技术系）；Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital（阿蒂努拉·A·马丁诺斯生物医学成像中心，麻省总医院）；Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology（麻省理工学院计算机科学与人工智能实验室）；Department of Radiology, Harvard Medical School（哈佛医学院放射学系）；Hawkes Institute, University College London（霍克斯研究所，伦敦大学学院）
Jesper Duemose Nielsen, Karthik Gopinath, Andrew Hoopes, Adrian Dalca, Axel Thielscher, Juan Eugenio Iglesias, Oula Puonti
Surface-based cortical analysis is useful in many applications as it is a natural way to model the highly folded structure of the cerebral cortex, allowing quantities such as curvature and thickness to be easily calculated. Existing deep learning (DL) methods have focused on 1x1x1 mm3 T1-weighted (T1w) scans, thus replicating classical pipelines. Here we present a neural network that is trained exclusively on synthetic scans with random contrast and resolution. Consequently, it can be applied to almost any kind of magnetic resonance imaging (MRI) scan. In addition, our model provides vertex-wise uncertainty estimates of the predicted surface as well as a spherical registration to fsaverage space. Our model performs on par with other state-of-the-art DL methods on 1x1x1 mm3 T1w scans and outperforms the only other method capable of estimating cortical surfaces from low resolution, non-T1w scans. The predicted uncertainty, moreover, correlates with overall scan quality on low resolution scans and highlights areas of poor surface reconstruction on 1x1x1 mm3 T1w scans, suggesting that it can be used for quality control. Finally, the predicted spherical registrations prove comparable to other DL and classical registration methods. These qualities, when combined with the fast inference time, will provide the ability to analyze large, existing databases of clinical MRI scans, with the potential for finding disease-specific patterns that would otherwise be infeasible in a research setting.
Rheinische Friedrich-Wilhelms-Universität Bonn（波恩大学）；Hôpitaux Universitaires de Genève（日内瓦大学医院）
Brain shift, i.e. the change in configuration of the brain after opening the dura mater, is a key problem in neuronavigation. We present an approach to co-register intra-operative microscope images with pre-operative MRI to adapt and optimize intra-operative neuronavigation. The tools are a robust classification of sulci on MRI extracted cortical surfaces, guided user marking of most prominent sulci on a microscope image, and the actual variational registration method with a fidelity energy for 3D deformations of the cortical surface combined with a higher order, linear elastica type prior ene…
Recon-all-clinical: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI
Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Copenhagen University Hospital - Amager and Hvidovre（哥本哈根大学医院阿莫尔与维杜夫院区）；Danish Research Centre for Magnetic Resonance（丹麦磁共振研究中心）；Centre for Functional and Diagnostic Imaging and Research（功能与诊断成像及研究中心）
Fetal cortical plate segmentation is essential in quantitative analysis of fetal brain maturation and cortical folding. Manual segmentation of the cortical plate, or manual refinement of automatic segmentations is tedious and time-consuming. Automatic segmentation of the cortical plate, on the other hand, is challenged by the relatively low resolution of the reconstructed fetal brain MRI scans compared to the thin structure of the cortical plate, partial voluming, and the wide range of variations in the morphology of the cortical plate as the brain matures during gestation. To reduce the burde…
Technische Universität München（慕尼黑工业大学）；Konica Minolta Laboratory Europe（柯尼卡美能达欧洲实验室）；Johns Hopkins University（约翰斯·霍普金斯大学）；Trinity College Dublin（都柏林圣三一学院）
Registration of partial-view 3D US volumes with MRI data is influenced by initialization. The standard of practice is using extrinsic or intrinsic landmarks, which can be very tedious to obtain. To overcome the limitations of registration initialization, we present a novel approach that is based on Euclidean distance maps derived from easily obtainable coarse segmentations. We evaluate our approach quantitatively on the publicly available RESECT dataset and show that it is robust regarding overlap of target area and initial position. Furthermore, our method provides initializations that are su…
The human cortical layer exhibits a convoluted morphology that is unique to each individual. Conventional volumetric fMRI processing schemes take for granted the rich information provided by the underlying anatomy. We present a method to study fMRI data on subject-specific cerebral hemisphere cortex (CHC) graphs, which encode the cortical morphology at the resolution of voxels in 3-D. We study graph spectral energy metrics associated to fMRI data of 100 subjects from the Human Connectome Project database, across seven tasks. Experimental results signify the strength of CHC graphs' Laplacian ei…
Center for Image Sciences, University Medical Center Utrecht, the Netherlands（荷兰乌得勒支大学医学中心影像科学中心）；Department of Radiology, University Medical Center Utrecht, the Netherlands（荷兰乌得勒支大学医学中心放射科）
Motion correction of dynamic contrast enhanced magnetic resonance images (DCE-MRI) is a challenging task, due to changes in image appearance. In this study a groupwise registration, using a principle component analysis (PCA) based metric,1 is evaluated for clinical DCE MRI of the liver. The groupwise registration transforms the images to a common space, rather than to a reference volume as conventional pairwise methods do, and computes the similarity metric on all volumes simultaneously. This groupwise registration method is compared to a pairwise approach using a mutual information metric. Cl…
GSMorph: Gradient Surgery for cine-MRI Cardiac Deformable Registration
University of Leeds（利兹大学）；Radboud University Medical Centre（拉德堡德大学医学中心）；Netherlands Cancer Institute（荷兰癌症研究所）；Shenzhen University（深圳大学）；Shenzhen RayShape Medical Technology Co., Ltd（深圳睿心医疗科技有限公司）
Learning accurate rigid registration for longitudinal brain MRI from synthetic data
1 Division of Biomedical Imaging, KTH Royal Institute of Technology, Huddinge, Sweden 2 Athinoula A.\ Martinos Center for Biomedical Imaging, Charlestown, USA 3 Department of Radiology, Massachusetts General Hospital, Boston, USA 4 Department of Radiology, Harvard Medical School, Boston, USA 5 Computer Science \& Artificial Intelligence Laboratory, MIT, Cambridge, USA
The Chinese University of Hong Kong（香港中文大学）；Massachusetts Institute of Technology（麻省理工学院）
In medical imaging, surface registration is extensively used for performing systematic comparisons between anatomical structures, with a prime example being the highly convoluted brain cortical surfaces. To obtain a meaningful registration, a common approach is to identify prominent features on the surfaces and establish a low-distortion mapping between them with the feature correspondence encoded as landmark constraints. Prior registration works have primarily focused on using manually labeled landmarks and solving highly nonlinear optimization problems, which are time-consuming and hence hin…
Technical University of Munich（慕尼黑工业大学）；Ludwig-Maximilians-University Munich（慕尼黑路德维希-马克西米利安大学）
The reconstruction of cortical surfaces from brain magnetic resonance imaging (MRI) scans is essential for quantitative analyses of cortical thickness and sulcal morphology. Although traditional and deep learning-based algorithmic pipelines exist for this purpose, they have two major drawbacks: lengthy runtimes of multiple hours (traditional) or intricate post-processing, such as mesh extraction and topology correction (deep learning-based). In this work, we address both of these issues and propose Vox2Cortex, a deep learning-based algorithm that directly yields topologically correct, three-di…
Britton Chance Center for Biomedical Photonics（布里顿·钱斯生物医学光子学研究中心）；Wuhan National Laboratory for Optoelectronics（武汉光电国家研究中心）；MoE Key Laboratory for Biomedical Photonics（教育部生物医学光子学重点实验室）；Collaborative Innovation Center for Biomedical Engineering（生物医学工程协同创新中心）；School of Engineering Sciences, Huazhong University of Science and Technology（华中科技大学工程科学学院）
Registration of brain MRI images requires to solve a deformation field, which is extremely difficult in aligning intricate brain tissues, e.g., subcortical nuclei, etc. Existing efforts resort to decomposing the target deformation field into intermediate sub-fields with either tiny motions, i.e., progressive registration stage by stage, or lower resolutions, i.e., coarse-to-fine estimation of the full-size deformation field. In this paper, we argue that those efforts are not mutually exclusive, and propose a unified framework for robust brain MRI registration in both progressive and coarse-to-…
To deform or not: treatment-aware longitudinal registration for breast DCE-MRI during neoadjuvant chemotherapy via unsupervised keypoints detection
Radboud University Medical Centre（拉德堡德大学医学中心）；The Netherlands Cancer Institute（荷兰癌症研究所）；Macao Polytechnic University（澳门理工大学）；Maastricht University Medical Centre（马斯特里赫特大学医学中心）
Reutlingen University（罗伊特林根大学）；Menoufia University（梅努菲亚大学）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）
Reliable and accurate registration of patient-specific brain magnetic resonance imaging (MRI) scans containing pathologies is challenging due to tissue appearance changes. This paper describes our contribution to the Registration of the longitudinal brain MRI task of the Brain Tumor Sequence Registration Challenge 2022 (BraTS-Reg 2022). We developed an enhanced unsupervised learning-based method that extends the iRegNet. In particular, incorporating an unsupervised learning-based paradigm as well as several minor modifications to the network pipeline, allows the enhanced iRegNet method to achi…
JOSA: Joint surface-based registration and atlas construction of brain geometry and function
McGovern Institute for Brain Research, MIT（麦戈文脑科学研究所（麻省理工学院））；Harvard University（哈佛大学）；Computer Science and Artificial Intelligence Laboratory, MIT（计算机科学与人工智能实验室（麻省理工学院））
Ecole Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）；University of Lausanne（洛桑大学）；Lausanne University Hospital（洛桑大学医院）；National Institute of Neurological Disorders and Stroke（美国国家神经疾病与卒中研究所）；National Institutes of Health（美国国立卫生研究院）；University of Bern（伯尔尼大学）；University of Pennsylvania（宾夕法尼亚大学）；Cedars-Sinai Medical Center（西达赛奈医疗中心）
The automated detection of cortical lesions (CLs) in patients with multiple sclerosis (MS) is a challenging task that, despite its clinical relevance, has received very little attention. Accurate detection of the small and scarce lesions requires specialized sequences and high or ultra-high field MRI. For supervised training based on multimodal structural MRI at 7T, two experts generated ground truth segmentation masks of 60 patients with 2014 CLs. We implemented a simplified 3D U-Net with three resolution levels (3D U-Net-). By increasing the complexity of the task (adding brain tissue segmen…
University College London（伦敦大学学院）；Inria（法国国家信息与自动化研究所）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Massachusetts Institute of Technology（麻省理工学院）
Joint registration of a stack of 2D histological sections to recover 3D structure (``3D histology reconstruction'') finds application in areas such as atlas building and validation of \emph{in vivo} imaging. Straightforward pairwise registration of neighbouring sections yields smooth reconstructions but has well-known problems such as ``banana effect'' (straightening of curved structures) and ``z-shift'' (drift). While these problems can be alleviated with an external, linearly aligned reference (e.g., Magnetic Resonance (MR) images), registration is often inaccurate due to contrast difference…
TimeFlow: Temporal Conditioning for Longitudinal Brain MRI Registration and Aging Analysis
Technical University of Munich, TUM University Hospital（慕尼黑工业大学，慕尼黑工业大学附属医院）；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心）；Munich Data Science Institute (MDSI)（慕尼黑数据科学研究所）；Imperial College London（伦敦帝国理工学院）
Technische Universität München（慕尼黑工业大学）；ScintHealth GmbH（ScintHealth有限公司）；Reply SpA（Reply股份公司）；Helmholtz Zentrum München（慕尼黑亥姆霍兹中心）；Helmholtz AI（亥姆霍兹人工智能研究所）
CT and MRI are two of the most informative modalities in spinal diagnostics and treatment planning. CT is useful when analysing bony structures, while MRI gives information about the soft tissue. Thus, fusing the information of both modalities can be very beneficial. Registration is the first step for this fusion. While the soft tissues around the vertebra are deformable, each vertebral body is constrained to move rigidly. We propose a weakly-supervised deep learning framework that preserves the rigidity and the volume of each vertebra while maximizing the accuracy of the registration. To achi…
Diffeomorphic Multi-Resolution Deep Learning Registration for Applications in Breast MRI
Auckland Bioengineering Institute（奥克兰生物工程研究所）；University of Auckland（奥克兰大学）；Faculty of Medical and Health Sciences（医学与健康科学学院）；MGH/HST Martinos Center for Biomedical Imaging（麻省总医院/哈佛健康科学技术生物医学成像马蒂诺斯中心）；Harvard Medical School（哈佛医学院）；MIT（麻省理工学院）
Deformable image registration is a key task in medical image analysis. The Brain Tumor Sequence Registration challenge (BraTS-Reg) aims at establishing correspondences between pre-operative and follow-up scans of the same patient diagnosed with an adult brain diffuse high-grade glioma and intends to address the challenging task of registering longitudinal data with major tissue appearance changes. In this work, we proposed a two-stage cascaded network based on the Inception and TransMorph models. The dataset for each patient was comprised of a native pre-contrast (T1), a contrast-enhanced T1-w…
Erasmus MC（伊拉斯姆斯大学医学中心）；Delft University of Technology（代尔夫特理工大学）
This work presents a single-step deep-learning framework for longitudinal image analysis, coined Segis-Net. To optimally exploit information available in longitudinal data, this method concurrently learns a multi-class segmentation and nonlinear registration. Segmentation and registration are modeled using a convolutional neural network and optimized simultaneously for their mutual benefit. An objective function that optimizes spatial correspondence for the segmented structures across time-points is proposed. We applied Segis-Net to the analysis of white matter tracts from N=8045 longitudinal …
University College London（伦敦大学学院）；Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）；Allen Institute for Brain Science（艾伦脑科学研究所）；Massachusetts Institute of Technology（麻省理工学院）
Nonlinear registration of 2D histological sections with corresponding slices of MRI data is a critical step of 3D histology reconstruction. This task is difficult due to the large differences in image contrast and resolution, as well as the complex nonrigid distortions produced when sectioning the sample and mounting it on the glass slide. It has been shown in brain MRI registration that better spatial alignment across modalities can be obtained by synthesizing one modality from the other and then using intra-modality registration metrics, rather than by using mutual information (MI) as metric…
We present a robust method to correct for motion and deformations for in-utero volumetric MRI time series. Spatio-temporal analysis of dynamic MRI requires robust alignment across time in the presence of substantial and unpredictable motion. We make a Markov assumption on the nature of deformations to take advantage of the temporal structure in the image data. Forward message passing in the corresponding hidden Markov model (HMM) yields an estimation algorithm that only has to account for relatively small motion between consecutive frames. We demonstrate the utility of the temporal model by sh…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）
Method: ProRSeg was trained using 5-fold cross-validation with 110 T2-weighted MRI acquired at 5 treatment fractions from 10 different patients, taking care that same patient scans were not placed in training and testing folds. Segmentation accuracy was measured using Dice similarity coefficient (DSC) and Hausdorff distance at 95th percentile (HD95). Registration consistency was measured using coefficient of variation (CV) in displacement of OARs. Ablation tests and accuracy comparisons against multiple methods were done. Finally, applicability of ProRSeg to segment cone-beam CT (CBCT) scans w…
International Institute of Information Technology (IIIT)（国际信息技术学院）；McGill University（麦吉尔大学）；Sree Chitra Tirunal Institute for Medical Sciences and Technology（Sree Chitra Tirunal医学科学与技术研究所）
Segmentation of sub-cortical structures from MRI scans is of interest in many neurological diagnosis. Since this is a laborious task machine learning and specifically deep learning (DL) methods have become explored. The structural complexity of the brain demands a large, high quality segmentation dataset to develop good DL-based solutions for sub-cortical structure segmentation. Towards this, we are releasing a set of 114, 1.5 Tesla, T1 MRI scans with manual delineations for 14 sub-cortical structures. The scans in the dataset were acquired from healthy young (21-30 years) subjects ( 58 male a…
Massachusetts Institute of Technology（麻省理工学院）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；Washington University in St. Louis（圣路易斯华盛顿大学）；Shanghai Jiao Tong University（上海交通大学）
We present a robust method to correct for motion in volumetric in-utero MRI time series. Time-course analysis for in-utero volumetric MRI time series often suffers from substantial and unpredictable fetal motion. Registration provides voxel correspondences between images and is commonly employed for motion correction. Current registration methods often fail when aligning images that are substantially different from a template (reference image). To achieve accurate and robust alignment, we make a Markov assumption on the nature of motion and take advantage of the temporal smoothness in the imag…
MSR:Hybrid Field Modeling for CT-MRI Rigid-Deformable Registration of the Cervical Spine with an Annotated Dataset
School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China.（南方医科大学生物医学工程学院）；Guangdong Provincial Key Laboratory of Medical Image Processing, Guangzhou, 510515, China.（广东省医学图像处理重点实验室）；Guangdong Province Engineering Laboratory for Medical Imaging（广东省医学影像与诊断技术工程实验室）；Information Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.（南方医科大学南华医院信息中心）；Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China.（南方医科大学南华医院骨科脊柱外科）
Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) automatic 3-D registration is implemented and validated for small animal image volumes so that the high-resolution anatomical MRI information can be fused with the low spatial resolution of functional PET information for the localization of lesion that is currently in high demand in the study of tumor of cancer (oncology) and its corresponding preparation of pharmaceutical drugs. Though many registration algorithms are developed and applied on human brain volumes, these methods may not be as efficient on small animal datas…
Benchmarking and Explaining Deep Learning Cortical Lesion MRI Segmentation in Multiple Sclerosis
Faculty of Biology and Medicine, University of Lausanne (UNIL)（日内瓦大学生物与医学学院）；Radiology Department, Lausanne University Hospital (CHUV)（洛桑大学医院放射科）；MedGIFT, Institute of Informatics, School of Management, HES--SO Valais--Wallis University of Applied Sciences（应用科学与艺术西瓦利斯-瓦利斯大学信息学院）；CIBM Center for Biomedical Imaging（生物医学成像中心）；Department of Radiology and Medical Informatics, University of Geneva（日内瓦大学放射科与医学信息学系）；Translational Imaging in Neurology (ThINK) Basel, Department of Medicine and Biomedical Engineering, University Hospital Basel and University of Basel（神经学转化成像（ThINK）巴塞尔，巴塞尔大学医院和巴塞尔大学医学与生物医学工程系）；Multiple Sclerosis Center, Department of Neurology, University Hospital Basel（多发性硬化中心，巴塞尔大学医院神经科）；Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel and University of Basel（临床神经免疫学与神经科学巴塞尔研究中心（RC2NB），巴塞尔大学医院和巴塞尔大学）；Division of Radiological Physics, Department of Radiology, University Hospital Basel（放射物理学系，放射科，巴塞尔大学医院）；Department of Neurology, Icahn School of Medicine at Mount Sinai（伊坎医学院神经科）；Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health（神经疾病国家研究所转化神经放射学组，国家卫生研究院）；Neuroinflammation Imaging Lab (NIL), Université catholique de Louvain（神经炎症成像实验室（NIL），卢旺达大学）
Deformable Medical Image Registration with Effective Anatomical Structure Representation and Divide-and-Conquer Network
National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, School of Computer Science and Engineering, Northwestern Polytechnical University（集成空天地海大数据应用技术国家工程实验室，计算机科学与工程学院，西北工业大学）
Radiological imaging of prostate is becoming more popular among researchers and clinicians in searching for diseases, primarily cancer. Scans might be acquired at different times, with patient movement between scans, or with different equipment, resulting in multiple datasets that need to be registered. For this issue, we introduce a registration method using anatomical feature-guided mutual information. Prostate scans of the same patient taken in three different orientations are first aligned for the accurate detection of anatomical features in 3D. Then, our pipeline allows for multiple modal…
Deep learning and classical computer vision techniques in medical image analysis: Case studies on brain MRI tissue segmentation, lung CT COPD registration, and skin lesion classification
University of Exeter（埃克塞特大学）；Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）；Sorbonne Université（索邦大学）
GuidedMorph: Two-Stage Deformable Registration for Breast MRI
Department of Electrical and Computer Engineering, Duke University（电子工程系，杜克大学）；Department of Biostatistics & Bioinformatics, Duke University（生物统计学与生物信息学系，杜克大学）；Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida（健康结果与生物医学信息学系，医学院，佛罗里达大学）
Erasmus MC（伊拉斯姆斯医学中心）；Delft University of Technology（代尔夫特理工大学）
Analysis of longitudinal changes in imaging studies often involves both segmentation of structures of interest and registration of multiple timeframes. The accuracy of such analysis could benefit from a tailored framework that jointly optimizes both tasks to fully exploit the information available in the longitudinal data. Most learning-based registration algorithms, including joint optimization approaches, currently suffer from bias due to selection of a fixed reference frame and only support pairwise transformations. We here propose an analytical framework based on an unbiased learning strat…
GOUHFI 2.0: A Next-Generation Toolbox for Brain Segmentation and Cortex Parcellation at Ultra-High Field MRI
Department of Physics, Norwegian University of Science and Technology（挪威科学技术大学物理系）；Department of Radiology and Nuclear Medicine, St. Olavs Hospital HF（斯托尔奥斯医院HF放射科和核医学部）；Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital HF（斯托尔奥斯医院HF神经科和临床神经生理学部）；Department of Neuromedicine and Movement Science, St. Olavs Hospital HF（斯托尔奥斯医院HF神经医学与运动科学部）；Neuro-SysMed Center for Clinical Treatment Research, Department of Neurology, Haukeland University Hospital（Haukeland大学医院神经科临床治疗研究神经系医学中心）；Department of Clinical Medicine, University of Bergen（卑尔根大学临床医学系）；K.G. Jebsen Center for Translational Research in Parkinson’s disease, University of Bergen（帕金森病转化研究Jebsen中心，卑尔根大学）
Technion – Israel Institute of Technology（以色列理工学院）
Quantification of uncertainty in deep-neural-networks (DNN) based image registration algorithms plays a critical role in the deployment of image registration algorithms for clinical applications such as surgical planning, intraoperative guidance, and longitudinal monitoring of disease progression or treatment efficacy as well as in research-oriented processing pipelines. Currently available approaches for uncertainty estimation in DNN-based image registration algorithms may result in sub-optimal clinical decision making due to potentially inaccurate estimation of the uncertainty of the registr…
CNRS, University of Bordeaux, Bordeaux INP（法国国家科学研究中心、波尔多大学、波尔多综合理工学院）
Affine registration of one or several brain image(s) onto a common reference space is a necessary prerequisite for many image processing tasks, such as brain segmentation or functional analysis. Manual assessment of registration quality is a tedious and time-consuming task, especially in studies comprising a large amount of data. An automated and reliable quality control (QC) becomes mandatory. Moreover, the computation time of the QC must be also compatible with the processing of massive datasets. Therefore, an automated deep neural network approaches appear as a method of choice to automatic…
Université de Sherbrooke（舍布鲁克大学）；Xiamen University（厦门大学）；Centre Antoine Lacassagne（安托万·拉卡萨涅中心）；Université de Bourgogne Franche-Comté（勃艮第-弗朗什-孔泰大学）
In this paper, we propose a fully automatic MRI cardiac segmentation method based on a novel deep convolutional neural network (CNN) designed for the 2017 ACDC MICCAI challenge. The novelty of our network comes with its embedded shape prior and its loss function tailored to the cardiac anatomy. Our model includes a cardiac centerof-mass regression module which allows for an automatic shape prior registration. Also, since our method processes raw MR images without any manual preprocessing and/or image cropping, our CNN learns both high-level features (useful to distinguish the heart from other …
Escola Politécnica, Universidade de São Paulo（圣保罗大学理工学院）；Brain Institute, IIEP Albert Einstein（阿尔伯特·爱因斯坦教育与研究学院脑研究所）；Faculdade de Medicina, Universidade de São Paulo（圣保罗大学医学院）；University of California San Francisco（加州大学旧金山分校）；University of Würzburg（维尔茨堡大学）；Athinoula A. Martinos Center for Biomedical Imaging, MGH/HST（麻省总医院/哈佛-麻省理工健康科学与技术部阿西诺拉·A·马丁诺斯生物医学成像中心）
Although the latest advances in MRI technology have allowed the acquisition of higher resolution images, reliable delineation of cytoarchitectural or subcortical nuclei boundaries is not possible. As a result, histological images are still required to identify the exact limits of neuroanatomical structures. However, histological processing is associated with tissue distortion and fixation artifacts, which prevent a direct comparison between the two modalities. Our group has previously proposed a histological procedure based on celloidin embedding that reduces the amount of artifacts and yields…
BrainMorph: A Foundational Keypoint Model for Robust and Flexible Brain MRI Registration
Department of Radiology, Weill Cornell Medicine, New York City, NY, USA（韦尔·科恩医学中心放射科）；School of Electrical and Computer Engineering, Cornell University, Ithaca, NY, USA（康奈尔大学电气与计算机工程学院）；Computer Science and Artificial Intelligence Lab at the Massachusetts Institute of Technology, Cambridge, MA, USA（麻省理工学院计算机科学与人工智能实验室）
本文提出基于 KeyMorph 的 BrainMorph 关键点基础模型，利用超十万个 3D 脑 MRI 体积训练，实现鲁棒、可解释、快速可控的多模态成对与组级刚性、仿射及非线性配准。
Beyond the LUMIR challenge: The pathway to foundational registration models
The Russell H. Morgan Department of Radiology（Russell H. Morgan放射科）；Radiological Science, Johns Hopkins Medical School（约翰霍普金斯医学院放射科学）；Department of Computer Science, Aalto University（阿尔托大学计算机科学系）；Cornell University（康奈尔大学）；Canon Medical Systems (China) Co. Ltd.（佳能医疗系统（中国）有限公司）；School of Biomedical Engineering, Shenzhen University Medical School（深圳大学医学院生物医学工程学院）；Department of Imaging Physics, Delft University of Technology（代尔夫特理工大学成像物理系）；Technical University of Munich（慕尼黑技术大学）；Radboud University Medical Center（拉德伯德大学医学中心）；Inria, Paris, France（法国巴黎Inria）
AtlasSeg: Atlas Prior Guided Dual-U-Net for Cortical Segmentation in Fetal Brain MRI
College of Biomedical Engineering & Instrument Science, Zhejiang University（浙江大学生物医学工程与仪器科学学院）；Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences（中国医学科学院北京医院国家老年医学中心老年医学研究所）；Shandong Provincial Hospital Affiliated to Shandong First Medical University（山东第一医科大学附属山东省立医院）；State Key Lab of CAD&CG, Zhejiang University（浙江大学CAD&CG国家重点实验室）
Accurate and robust whole heart substructure segmentation is crucial in developing clinical applications, such as computer-aided diagnosis and computer-aided surgery. However, segmentation of different heart substructures is challenging because of inadequate edge or boundary information, the complexity of the background and texture, and the diversity in different substructures' sizes and shapes. This article proposes a framework for multi-class whole heart segmentation employing non-rigid registration-based probabilistic atlas incorporating the Bayesian framework. We also propose a non-rigid r…
Surface-volume self-supervised representation learning of brain MRI for genetic discovery
The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）；Yale School of Medicine（耶鲁大学医学院）；Texas A&M University（德克萨斯A&M大学）；Stanford University School of Medicine（斯坦福大学医学院）
