人类大脑在妊娠晚期会经历快速发育。本研究针对该年龄段的婴儿大脑新生儿期发育过程进行建模。研究以发育中人类连接组项目（developing human connectome project, dHCP）中的早产儿和足月儿磁共振（MR）图像为基础数据。提出了一种神经网络，具体为隐式神经表示（implicit neural representation, INR），用于预测不同时间点的2D和3D图像。为了建模受试者特异性的发育过程，需要在INR的潜在空间中将年龄与受试者身份解耦。为此提出了两种方法：受试者特异性潜在向量（Subject Specific Latent Vectors, SSL）和随机全局潜在增强（Stochastic Global Latent Augmentation, SGLA），以实现这种解耦。研究对结果进行了分析，并将所提模型与作为基线的年龄条件去噪扩散模型进行了对比。同时还表明，该方法可以以内存高效的方式应用，这一点对于3D数据尤为重要。
英文摘要：
The human brain undergoes rapid development during the third trimester of pregnancy. In this work, we model the neonatal development of the infant brain in this age range. As a basis, we use MR images of preterm- and term-birth neonates from the developing human connectome project (dHCP). We propose a neural network, specifically an implicit neural representation (INR), to predict 2D- and 3D images of varying time points. In order to model a subject-specific development process, it is necessary to disentangle the age from the subjects' identity in the latent space of the INR. We propose two methods, Subject Specific Latent Vectors (SSL) and Stochastic Global Latent Augmentation (SGLA), enabling this disentanglement. We perform an analysis of the results and compare our proposed model to an age-conditioned denoising diffusion model as a baseline. We also show that our method can be applied in a memory-efficient way, which is especially important for 3D data.
Image Sciences Institute, University Medical Center Utrecht（乌得勒支大学医学中心图像科学研究所）；Wilhelmina Children’s Hospital, University Medical Center Utrecht（乌得勒支大学医学中心威廉明娜儿童医院）；Brain Center Rudolf Magnus, University Medical Center Utrecht（乌得勒支大学医学中心鲁道夫·马格努斯脑中心）
Automatic neonatal brain tissue segmentation in preterm born infants is a prerequisite for evaluation of brain development. However, automatic segmentation is often hampered by motion artifacts caused by infant head movements during image acquisition. Methods have been developed to remove or minimize these artifacts during image reconstruction using frequency domain data. However, frequency domain data might not always be available. Hence, in this study we propose a method for removing motion artifacts from the already reconstructed MR scans. The method employs a generative adversarial network…
Diffusion-based translation between unpaired spontaneous premature neonatal EEG and fetal MEG
Laboratoire de Mathématiques de Lens (LML), UR 2462, Université d'Artois（Lens数学实验室（LML），UR 2462，阿托瓦大学）；Department of Internal Medicine IV, University Hospital of Tübingen（第四内科部门，图宾根大学医院）；IDM/fMEG Center of the Helmholtz Center Munich, University of Tübingen, German Center for Diabetes Research (DZD)（慕尼黑海德堡中心IDM/fMEG中心，图宾根大学，糖尿病研究德国中心（DZD））；Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Interfaculty Centre for Pharmacogenomics and Pharma Research, Eberhard Karls University Tübingen（药学研究所，药学与生物化学部门，药基因组学与药学研究跨学科中心，图宾根埃伯哈德·卡尔斯大学）
MGA-Net: A Novel Mask-Guided Attention Neural Network for Precision Neonatal Brain Imaging
Biomedical Research；Innovation Institute of C\'adiz (INiBICA) Research Unit, Puerta del Mar University, C\'adiz, Spain；Division of Neonatology, Department of Pediatrics, Puerta del Mar University Hospital, C\'adiz, Spain；Area of Pediatrics, Department of Child；Radiology, Medical School, University of C\'adiz, C\'adiz, Spain
MELAGE: A purely python based Neuroimaging software (Neonatal)
Biomedical Research and Innovation Institute of Cádiz (INiBICA)（加的斯生物医学研究与创新研究所（INiBICA））；Puerta del Mar University Hospital（海洋之门大学医院）；University of Cádiz（加的斯大学）
Ground-truth effects in learning-based fiber orientation distribution estimation in neonatal brains
Signal Processing Laboratory (LTS5)（信号处理实验室）；École Polytechnique Fédérale de Lausanne (EPFL)（瑞士联邦理工学院洛桑分校）；Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL)（洛桑大学医院放射科及洛桑大学）；College of Electronic and Information Engineering, Tongji University（同济大学电子与信息学院）；CIBM Center for Biomedical Imaging（生物医学成像中心）；Computational Radiology Laboratory, Department of Radiology, Boston Children’s Hospital and Harvard Medical School（波士顿儿童医院放射科计算放射实验室及哈佛医学院）；Department of Radiological Sciences, University of California Irvine（加州大学 Irvine 分校放射科学系）
Resting state fMRI (rsfMRI) has been shown to be a promising tool to study intrinsic functional connectivity and assess its integrity in cerebral development. In neonates, where fMRI is limited to few paradigms, rsfMRI was shown to be a relevant tool to explore regional interactions of brain networks. However, to identify the resting state networks, data needs to be carefully processed. Because of the non-collaborative nature of the neonates, the differences in brain size and the reversed contrast compared to adults, neonates can't be processed with the existing adult pipelines. Therefore, we …
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）；National Institute on Aging（美国国家老龄化研究所）
An important task in image processing and neuroimaging is to extract quantitative information from the acquired images in order to make observations about the presence of disease or markers of development in populations. Having a lowdimensional manifold of an image allows for easier statistical comparisons between groups and the synthesis of group representatives. Previous studies have sought to identify the best mapping of brain MRI to a low-dimensional manifold, but have been limited by assumptions of explicit similarity measures. In this work, we use deep learning techniques to investigate …
Diffusion MRI (dMRI) of the developing brain can provide valuable insights into the white matter development. However, slice thickness in fetal dMRI is typically high (i.e., 3-5 mm) to freeze the in-plane motion, which reduces the sensitivity of the dMRI signal to the underlying anatomy. In this study, we aim at overcoming this problem by using autoencoders to learn unsupervised efficient representations of brain slices in a latent space, using raw dMRI signals and their spherical harmonics (SH) representation. We first learn and quantitatively validate the autoencoders on the developing Human…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
We present an empirical evaluation of fMRI data augmentation via synthesis. For synthesis we use generative mod-els trained on real neuroimaging data to produce novel task-dependent functional brain images. Analyzed generative mod-els include classic approaches such as the Gaussian mixture model (GMM), and modern implicit generative models such as the generative adversarial network (GAN) and the variational auto-encoder (VAE). In particular, the proposed GAN and VAE models utilize 3-dimensional convolutions, which enables modeling of high-dimensional brain image tensors with structured spatial…
UltraDfeGAN: Detail-Enhancing Generative Adversarial Networks for High-Fidelity Functional Ultrasound Synthesis
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Department of Information and Communication, Institute of Technology of Cambodia（柬埔寨技术学院信息与通信系）；Department of Telecommunication and Network Engineering, Institute of Technology of Cambodia（柬埔寨技术学院电信与网络工程系）
Diffusion Models for Counterfactual Generation and Anomaly Detection in Brain Images
University of Edinburgh（爱丁堡大学）；NHS Lothian（洛锡安国民保健服务体系）；UK Dementia Research Institute Centre, University of Edinburgh（英国痴呆症研究所爱丁堡中心）；University of Dundee（邓迪大学）
Image-to-Brain Signal Generation for Visual Prosthesis with CLIP Guided Multimodal Diffusion Models
Jinan University, Guangzhou, China；Department of Rehabilitation Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China；Western University, Ontario, Canada；Guangdong University of Technology, Guangzhou, China；Tsinghua University, Beijing, China
Recently, diffusion models were applied to a wide range of image analysis tasks. We build on a method for image-to-image translation using denoising diffusion implicit models and include a regression problem and a segmentation problem for guiding the image generation to the desired output. The main advantage of our approach is that the guidance during the denoising process is done by an external gradient. Consequently, the diffusion model does not need to be retrained for the different tasks on the same dataset. We apply our method to simulate the aging process on facial photos using a regress…
Longitudinal fetal brain atlas is a powerful tool for understanding and characterizing the complex process of fetus brain development. Existing fetus brain atlases are typically constructed by averaged brain images on discrete time points independently over time. Due to the differences in onto-genetic trends among samples at different time points, the resulting atlases suffer from temporal inconsistency, which may lead to estimating error of the brain developmental characteristic parameters along the timeline. To this end, we proposed a multi-stage deep-learning framework to tackle the time in…
Mechanistic Learning with Guided Diffusion Models to Predict Spatio-Temporal Brain Tumor Growth
ETH Zurich, 8092 Zurich, Switzerland - SIB Swiss Institue of Bioinformatics, 1015 Lausanne, Switzerland Department of Radiation Oncology, Inselspital, Bern University Hospital；University of Bern, Switzerland Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Medical Center, Washington, DC 20010, United States University of California San Francisco, San Francisco, CA 94143, United States University Children's Hospital Zurich, 8008 Zurich, Switzerland
Mass General Brigham, Harvard Medical School, MA, United States（马萨诸塞州总医院、哈佛医学院）；Department of Statistics, University of South Carolina, SC, United States（统计学系，南卡罗来纳大学）；Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, MA, United States（解剖学与神经生物学系，波士顿大学钱德林与阿维迪亚安医学学院）；Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, MA, United States（阿提诺拉A·马丁诺斯生物医学成像中心，马萨诸塞总医院）；Department of Radiology, Harvard Medical School, MA, United States（放射学系，哈佛医学院）；Harvard/MIT Health Sciences and Technology, MA, United States（哈佛/麻省理工健康科学与技术）
King’s College London（伦敦国王学院）；University Hospitals Leuven（鲁汶大学医院）；Technical University of Munich（慕尼黑工业大学）；University College London（伦敦大学学院）
This paper describes our method for our participation in the FeTA challenge2021 (team name: TRABIT). The performance of convolutional neural networks for medical image segmentation is thought to correlate positively with the number of training data. The FeTA challenge does not restrict participants to using only the provided training data but also allows for using other publicly available sources. Yet, open access fetal brain data remains limited. An advantageous strategy could thus be to expand the training data to cover broader perinatal brain imaging sources. Perinatal brain MRIs, other tha…
Meta-learning Slice-to-Volume Reconstruction in Fetal Brain MRI using Implicit Neural Representations
School of Computation, Information and Technology, and School of Medicine and Health, Technical University Munich（计算、信息与技术学院，以及医学与健康学院，技术大学慕尼黑）；CIBM Center for Biomedical Imaging and Radiology Department of Lausanne University Hospital and University of Lausanne（日内瓦大学医院与日内瓦大学生物医学影像与放射学中心部门）；Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London（发展脑中心，生物医学工程与影像科学学院，伦敦国王学院）；Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid（生物医学影像技术，电信工程学院，马德里理工大学）；Department of Computing, Imperial College London（计算学院，伦敦帝国学院）
City, University of London（伦敦大学城市学院）；Imperial College（帝国理工学院）
We propose a novel unsupervised out-of-distribution detection method for medical images based on implicit fields image representations. In our approach, an auto-decoder feed-forward neural network learns the distribution of healthy images in the form of a mapping between spatial coordinates and probabilities over a proxy for tissue types. At inference time, the learnt distribution is used to retrieve, from a given test image, a restoration, i.e. an image maximally consistent with the input one but belonging to the healthy distribution. Anomalies are localized using the voxel-wise probability p…
Implicit neural representations (INR) have been recently proposed as deep learning (DL) based solutions for image compression. An image can be compressed by training an INR model with fewer weights than the number of image pixels to map the coordinates of the image to corresponding pixel values. While traditional training approaches for INRs are based on enforcing pixel-wise image consistency, we propose to further improve image quality by using a new structural regularizer. We present structural regularization for INR compression (SINCO) as a novel INR method for image compression. SINCO impo…
Henry M. Jackson Foundation（亨利·M·杰克逊基金会）；Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）
In 2D multi-slice magnetic resonance (MR) acquisition, the through-plane signals are typically of lower resolution than the in-plane signals. While contemporary super-resolution (SR) methods aim to recover the underlying high-resolution volume, the estimated high-frequency information is implicit via end-to-end data-driven training rather than being explicitly stated and sought. To address this, we reframe the SR problem statement in terms of perfect reconstruction filter banks, enabling us to identify and directly estimate the missing information. In this work, we propose a two-stage approach…
Implicit neural representations for end-to-end PET reconstruction
Nantes Université（南特大学）；École Centrale Nantes（南特中央理工学院）；CNRS（法国国家科学研究中心）；Centre Hospitalier Universitaire de Nantes（南特大学医院中心）；INSERM（法国国家健康与医学研究院）；Université d'Angers（昂热大学）；CRCI2NA
InverseSR: 3D Brain MRI Super-Resolution Using a Latent Diffusion Model
St. Francis Xavier University（圣弗朗西斯泽维尔大学）；Martinos Center for Biomedical Imaging（马蒂诺生物医学成像中心）；Massachusetts General Hospital（麻省总医院）；Nova Scotia Health Authority（新斯科舍省卫生局）；King’s College London（伦敦国王学院）；University of California, Santa Cruz（加州大学圣克鲁兹分校）
Single-Subject Multi-View MRI Super-Resolution via Implicit Neural Representations
Department of Radiology, Weill Cornell Medicine, New York, USA（韦尔·科恩医学系放射科，纽约，美国）；School of Electrical and Computer Engineering, Cornell University（康奈尔大学电气与计算机工程学院）；Cornell Tech, New York, USA（康奈尔科技，纽约，美国）；Weill Cornell Graduate School of Medical Sciences, New York, USA（韦尔·科恩医学科学研究生院，纽约，美国）
From Coarse to Continuous: Progressive Refinement Implicit Neural Representation for Motion-Robust Anisotropic MRI Reconstruction
Department of Bioengineering and Imperial-X, Imperial College London（生物工程系和Imperial-X，帝国理工学院伦敦分校）；Department of Bioengineering, Imperial College London（生物工程系，帝国理工学院伦敦分校）
