Diffusion magnetic resonance imaging datasets suffer from low Signal-to-Noise Ratio, especially at high b-values. Acquiring data at high b-values contains relevant information and is now of great interest for microstructural and connectomics studies. High noise levels bias the measurements due to the non-Gaussian nature of the noise, which in turn can lead to a false and biased estimation of the diffusion parameters. Additionally, the usage of in-plane acceleration techniques during the acquisition leads to a spatially varying noise distribution, which depends on the parallel acceleration method implemented on the scanner. This paper proposes a novel diffusion MRI denoising technique that can be used on all existing data, without adding to the scanning time. We first apply a statistical framework to convert the noise to Gaussian distributed noise, effectively removing the bias. We then introduce a spatially and angular adaptive denoising technique, the Non Local Spatial and Angular Matching (NLSAM) algorithm. Each volume is first decomposed in small 4D overlapping patches to capture the structure of the diffusion data and a dictionary of atoms is learned on those patches. A local sparse decomposition is then found by bounding the reconstruction error with the local noise variance. We compare against three other state-of-the-art denoising methods and show quantitative local and connectivity results on a synthetic phantom and on an in-vivo high resolution dataset. Overall, our method restores perceptual information, removes the noise bias in common diffusion metrics, restores the extracted peaks coherence and improves reproducibility of tractography. Our work paves the way for higher spatial resolution acquisition of diffusion MRI datasets, which could in turn reveal new anatomical details that are not discernible at the spatial resolution currently used by the diffusion MRI community.
Indraprastha Institute of Information Technology（英迪拉·普拉斯特哈信息技术研究所）
In this work we address the problem of real-time dynamic MRI reconstruction. There are a handful of studies on this topic; these techniques are either based on compressed sensing or employ Kalman Filtering. These techniques cannot achieve the reconstruction speed necessary for real-time reconstruction. In this work, we propose a new approach to MRI reconstruction. We learn a non-linear mapping from the unstructured aliased images to the corresponding clean images using a stacked denoising autoencoder (SDAE). The training for SDAE is slow, but the reconstruction is very fast - only requiring a …
Eindhoven University of Technology（埃因霍温理工大学）；Philips Research（飞利浦研究院）
Ultrasonography offers an inexpensive, widely-accessible and compact medical imaging solution. However, compared to other imaging modalities such as CT and MRI, ultrasound images notoriously suffer from strong speckle noise, which originates from the random interference of sub-wavelength scattering. This deteriorates ultrasound image quality and makes interpretation challenging. We here propose a new unsupervised ultrasound speckle reduction and image denoising method based on maximum-a-posteriori estimation with deep generative priors that are learned from high-quality MRI images. To model th…
Self-Supervised Diffusion MRI Denoising via Iterative and Stable Refinement
School of Biomedical Engineering, Division of Life Sciences and Medicine, USTC（中国科学技术大学生命科学与医学部生物医学工程学院）；MIRACLE Center, Suzhou Institute for Advance Research, USTC（中国科学技术大学苏州研究院MIRACLE中心）；State Key Laboratory of Precision and Intelligent Chemistry, USTC（中国科学技术大学精准与智能化学国家重点实验室）；Key Laboratory of Intelligent Information Processing of CAS, Institute of Computing Technology, CAS（中国科学院计算技术研究所中国科学院智能信息处理重点实验室）
Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled traini…
Hybrid Learning: A Novel Combination of Self-Supervised and Supervised Learning for Joint MRI Reconstruction and Denoising in Low-Field MRI
New York University Grossman School of Medicine（纽约大学格罗斯曼医学院）；NYU Tandon School of Engineering（纽约大学坦登工程学院）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）
Arterial spin labeling (ASL) allows to quantify the cerebral blood flow (CBF) by magnetic labeling of the arterial blood water. ASL is increasingly used in clinical studies due to its noninvasiveness, repeatability and benefits in quantification. However, ASL suffers from an inherently low-signal-to-noise ratio (SNR) requiring repeated measurements of control/spin-labeled (C/L) pairs to achieve a reasonable image quality, which in return increases motion sensitivity. This leads to clinically prolonged scanning times increasing the risk of motion artifacts. Thus, there is an immense need of adv…
Indiana University Bloomington（印第安纳大学伯明顿分校）；CZ Biohub（CZ生物中心）
Diffusion-weighted magnetic resonance imaging (DWI) is the only noninvasive method for quantifying microstructure and reconstructing white-matter pathways in the living human brain. Fluctuations from multiple sources create significant additive noise in DWI data which must be suppressed before subsequent microstructure analysis. We introduce a self-supervised learning method for denoising DWI data, Patch2Self, which uses the entire volume to learn a full-rank locally linear denoiser for that volume. By taking advantage of the oversampled q-space of DWI data, Patch2Self can separate structure f…
Robust multi-coil MRI reconstruction via self-supervised denoising
Stanford University（斯坦福大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）；Intel Corporation（英特尔公司）；MD Anderson Cancer Center（MD安德森癌症中心）；Dell Medical School Department of Diagnostic Medicine（德克萨斯大学戴维斯医学中心诊断医学系）；Oden Institute for Computational Engineering and Sciences（奥登计算工程与科学研究院）
Counterfactual MRI Data Augmentation using Conditional Denoising Diffusion Generative Models
Instituto Superior Técnico（高等技术学院）；Universidade de Lisboa（里斯本大学）；Digital Surgery LAB（数字外科实验室）；Champalimaud Foundation（尚帕利莫基金会）；Faculdade de Medicina, Universidade de Lisboa（里斯本大学医学院）；Instituto de Telecomunicações（电信研究所）
Self-Supervised Joint Reconstruction and Denoising of T2-Weighted PROPELLER MRI of the Lungs at 0.55T
New York University Grossman School of Medicine（纽约大学格罗斯曼医学院）；New York University Tandon School of Engineering（纽约大学坦登工程学院）；Indiana University School of Medicine（印第安纳大学医学院）
Ayandegan Institute of Higher Education（阿扬德甘高等教育学院）；The University of New South Wales（新南威尔士大学）
In this paper, a filtering approach for the 3D magnetic resonance imaging (MRI) assuming a Rician model for noise is addressed. Our denoising method is based on the Conventional Approach (CA) proposed to deal with the noise issue in the squared domain of the acquired magnitude MRI, where the noise distribution follows a Chi-square model rather than the Rician one. In the CA filtering method, the local samples around each voxel is used to estimate the unknown signal value. Intrinsically, such a method fails to achieve the best results where the underlying signal values have different statistica…
Peking University（北京大学）；Academy for Advanced Interdisciplinary Studies（前沿交叉学科研究院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
We propose a novel and unified method, measurement-conditioned denoising diffusion probabilistic model (MC-DDPM), for under-sampled medical image reconstruction based on DDPM. Different from previous works, MC-DDPM is defined in measurement domain (e.g. k-space in MRI reconstruction) and conditioned on under-sampling mask. We apply this method to accelerate MRI reconstruction and the experimental results show excellent performance, outperforming full supervision baseline and the state-of-the-art score-based reconstruction method. Due to its generative nature, MC-DDPM can also quantify the unce…
Inference Stage Denoising for Undersampled MRI Reconstruction
School of Engineering, The University of Edinburgh（爱丁堡大学工程学院）；Department of Electrical and Electronic Engineering and I-X, Imperial College London（帝国理工学院电气与电子工程系及I-X）
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；Graz University of Technology（格拉茨工业大学）；GE Healthcare（GE医疗）
Purpose: To investigate feasibility of accelerating prostate diffusion-weighted imaging (DWI) by reducing the number of acquired averages and denoising the resulting image using a proposed guided denoising convolutional neural network (DnCNN). Materials and Methods: Raw data from the prostate DWI scans were retrospectively gathered (between July 2018 and July 2019) from six single-vendor MRI scanners. 118 data sets were used for training and validation (age: 64.3 +- 8 years) and 37 - for testing (age: 65.1 +- 7.3 years). High b-value diffusion-weighted (hb-DW) data were reconstructed into nois…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）
We developed a new joint probabilistic segmentation and image distribution matching generative adversarial network (PSIGAN) for unsupervised domain adaptation (UDA) and multi-organ segmentation from magnetic resonance (MRI) images. Our UDA approach models the co-dependency between images and their segmentation as a joint probability distribution using a new structure discriminator. The structure discriminator computes structure of interest focused adversarial loss by combining the generated pseudo MRI with probabilistic segmentations produced by a simultaneously trained segmentation sub-networ…
University College London（伦敦大学学院）；Technion -- Israel Institute of Technology（以色列理工学院）；Heriot-Watt University（赫瑞-瓦特大学）
Medical imaging tasks often involve multiple contrasts, such as T1- and T2-weighted magnetic resonance imaging (MRI) data. These contrasts capture information associated with the same underlying anatomy and thus exhibit similarities. In this paper, we propose a Coupled Dictionary Learning based multi-contrast MRI reconstruction (CDLMRI) approach to leverage an available guidance contrast to restore the target contrast. Our approach consists of three stages: coupled dictionary learning, coupled sparse denoising, and $k$-space consistency enforcing. The first stage learns a group of dictionaries…
Automatic segmentation of the heart cavity is an essential task for the diagnosis of cardiac diseases. In this paper, we propose a semi-supervised segmentation setup for leveraging unlabeled data to segment Left-ventricle, Right-ventricle, and Myocardium. We utilize an enhanced version of residual U-Net architecture on a large-scale cardiac MRI dataset. Handling the class imbalanced data issue using dice loss, the enhanced supervised model is able to achieve better dice scores in comparison with a vanilla U-Net model. We applied several augmentation techniques including histogram matching to i…
Self-supervised training of deep denoisers in multi-coil MRI considering noise correlations
Department of Electrical and Computer Engineering, Seoul National University（电气电子工程系，首尔国立大学）；INMC & IPAI, Seoul National University（INMC与IPAI，首尔国立大学）；Division of Computer Engineering, Hankuk University of Foreign Studies（计算机工程系，韩文大学）；Department of Radiology, Johns Hopkins University School of Medicine（放射科，约翰霍普金斯大学医学院）
Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising…
Unified 3D MRI Representations via Sequence-Invariant Contrastive Learning
Department of Imaging Neuroscience, University College London, UK（影像神经科学系，伦敦大学学院，英国）；Institute of Cognitive Neuroscience, University College London, UK（认知神经科学研究所，伦敦大学学院，英国）
University of Bath（巴斯大学）；Imago7 foundation（Imago7基金会）；University of Edinburgh（爱丁堡大学）；GE Healthcare（GE医疗）；Technical University of Munich（慕尼黑工业大学）
We propose a dictionary-matching-free pipeline for multi-parametric quantitative MRI image computing. Our approach has two stages based on compressed sensing reconstruction and deep learned quantitative inference. The reconstruction phase is convex and incorporates efficient spatiotemporal regularisations within an accelerated iterative shrinkage algorithm. This minimises the under-sampling (aliasing) artefacts from aggressively short scan times. The learned quantitative inference phase is purely trained on physical simulations (Bloch equations) that are flexible for producing rich training sa…
Indian Institute of Information Technology Vadodara（瓦多达拉印度信息技术学院）
Medical image acquisition is often intervented by unwanted noise that corrupts the information content. This paper introduces an unsupervised medical image denoising technique that learns noise characteristics from the available images and constructs denoised images. It comprises of two blocks of data processing, viz., patch-based dictionaries that indirectly learn the noise and residual learning (RL) that directly learns the noise. The model is generalized to account for both 2D and 3D images considering different medical imaging instruments. The images are considered one-by-one from the stac…
We develop a Bayesian nonparametric model for reconstructing magnetic resonance images (MRI) from highly undersampled k-space data. We perform dictionary learning as part of the image reconstruction process. To this end, we use the beta process as a nonparametric dictionary learning prior for representing an image patch as a sparse combination of dictionary elements. The size of the dictionary and the patch-specific sparsity pattern are inferred from the data, in addition to other dictionary learning variables. Dictionary learning is performed directly on the compressed image, and so is tailor…
Rician Denoising Diffusion Probabilistic Models For Sodium Breast MRI Enhancement
University of Cambridge（剑桥大学）；Universitat de Barcelona（巴塞罗那大学）；Haukeland University Hospital（豪克兰大学医院）；University of York（约克大学）；Manchester Metropolitan University（曼彻斯特城市大学）
Arterial spin labeling perfusion MRI is a noninvasive technique for measuring quantitative cerebral blood flow (CBF), but the measurement is subject to a low signal-to-noise-ratio(SNR). Various post-processing methods have been proposed to denoise ASL MRI but only provide moderate improvement. Deep learning (DL) is an emerging technique that can learn the most representative signal from data without prior modeling which can be highly complex and analytically indescribable. The purpose of this study was to assess whether the record breaking performance of DL can be translated into ASL MRI denoi…
Cycle-guided Denoising Diffusion Probability Model for 3D Cross-modality MRI Synthesis
Emory University（埃默里大学）；Winship Cancer Institute（温希普癌症研究所）；Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）
Politecnico di Milano（米兰理工大学）；University of Twente（特温特大学）；University of Bath（巴斯大学）；University of Cambridge（剑桥大学）
4D flow MRI is a non-invasive imaging method that can measure blood flow velocities over time. However, the velocity fields detected by this technique have limitations due to low resolution and measurement noise. Coordinate-based neural networks have been researched to improve accuracy, with SIRENs being suitable for super-resolution tasks. Our study investigates SIRENs for time-varying 3-directional velocity fields measured in the aorta by 4D flow MRI, achieving denoising and super-resolution. We trained our method on voxel coordinates and benchmarked our approach using synthetic measurements…
DiffCMR: Fast Cardiac MRI Reconstruction with Diffusion Probabilistic Models
The Hong Kong University of Science and Technology（香港科技大学）；Southern University of Science and Technology（南方科技大学）；HKUST Shenzhen Research Institute（香港科技大学深圳研究院）
There are two main streams in up-to-date image denoising algorithms: non-local self similarity (NSS) prior based methods and convolutional neural network (CNN) based methods. The NSS based methods are favorable on images with regular and repetitive patterns while the CNN based methods perform better on irregular structures. In this paper, we propose a block-matching convolutional neural network (BMCNN) method that combines NSS prior and CNN. Initially, similar local patches in the input image are integrated into a 3D block. In order to prevent the noise from messing up the block matching, we f…
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 …
Johns Hopkins University（约翰斯·霍普金斯大学）；The Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳））
The ultimate aim of image restoration like denoising is to find an exact correlation between the noisy and clear image domains. But the optimization of end-to-end denoising learning like pixel-wise losses is performed in a sample-to-sample manner, which ignores the intrinsic correlation of images, especially semantics. In this paper, we introduce the Deep Semantic Statistics Matching (D2SM) Denoising Network. It exploits semantic features of pretrained classification networks, then it implicitly matches the probabilistic distribution of clear images at the semantic feature space. By learning t…
The non-local self-similarity property of natural images has been exploited extensively for solving various image processing problems. When it comes to video sequences, harnessing this force is even more beneficial due to the temporal redundancy. In the context of image and video denoising, many classically-oriented algorithms employ self-similarity, splitting the data into overlapping patches, gathering groups of similar ones and processing these together somehow. With the emergence of convolutional neural networks (CNN), the patch-based framework has been abandoned. Most CNN denoisers operat…
WFM: 3D Wavelet Flow Matching for Ultrafast Multi-Modal MRI Synthesis
Department of Computer Science, Stanford University（斯坦福大学计算机科学系）；Machine and Hybrid Intelligence Lab, Feinberg School of Medicine, Northwestern University（北western大学费因伯格医学院机器与混合智能实验室）
本文提出WFM方法，通过学习基于小波空间条件均值的直接流，实现高效多模态MRI合成，单模型在BraTS 2024上达到26.8 dB PSNR和0.94 SSIM，速度比扩散模型快250-1000倍。
