Magnetic Resonance Fingerprinting (MRF) enables simultaneous mapping of multiple tissue parameters such as T1 and T2 relaxation times. The working principle of MRF relies on varying acquisition parameters pseudo-randomly, so that each tissue generates its unique signal evolution during scanning. Even though MRF provides faster scanning, it has disadvantages such as erroneous and slow generation of the corresponding parametric maps, which needs to be improved. Moreover, there is a need for explainable architectures for understanding the guiding signals to generate accurate parametric maps. In this paper, we addressed both of these shortcomings by proposing a novel neural network architecture consisting of a channel-wise attention module and a fully convolutional network. The proposed approach, evaluated over 3 simulated MRF signals, reduces error in the reconstruction of tissue parameters by 8.88% for T1 and 75.44% for T2 with respect to state-of-the-art methods. Another contribution of this study is a new channel selection method: attention-based channel selection. Furthermore, the effect of patch size and temporal frames of MRF signal on channel reduction are analyzed by employing a channel-wise attention.
University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Case Western Reserve University（凯斯西储大学）
Magnetic resonance Fingerprinting (MRF) is a relatively new multi-parametric quantitative imaging method that involves a two-step process: (i) reconstructing a series of time frames from highly-undersampled non-Cartesian spiral k-space data and (ii) pattern matching using the time frames to infer tissue properties (e.g., T1 and T2 relaxation times). In this paper, we introduce a novel end-to-end deep learning framework to seamlessly map the tissue properties directly from spiral k-space MRF data, thereby avoiding time-consuming processing such as the nonuniform fast Fourier transform (NUFFT) a…
Imperial College London（帝国理工学院）；Weizmann Institute of Science（魏茨曼科学研究所）；Technion – Israel Institute of Technology（以色列理工学院）；University College London（伦敦大学学院）
Purpose: Magnetic resonance fingerprinting (MRF) methods typically rely on dictio-nary matching to map the temporal MRF signals to quantitative tissue parameters. Such approaches suffer from inherent discretization errors, as well as high computational complexity as the dictionary size grows. To alleviate these issues, we propose a HYbrid Deep magnetic ResonAnce fingerprinting approach, referred to as HYDRA. Methods: HYDRA involves two stages: a model-based signature restoration phase and a learning-based parameter restoration phase. Signal restoration is implemented using low-rank based de-al…
Magnetic Resonance Fingerprinting (MRF) is an imaging technique acquiring unique time signals for different tissues. Although the acquisition is highly accelerated, the reconstruction time remains a problem, as the state-of-the-art template matching compares every signal with a set of possible signals. To overcome this limitation, deep learning based approaches, e.g. Convolutional Neural Networks (CNNs) have been proposed. In this work, we investigate the applicability of Recurrent Neural Networks (RNNs) for this reconstruction problem, as the signals are correlated in time. Compared to previo…
University of Edinburgh（爱丁堡大学）；University of Bath（巴斯大学）
Consistency of the predictions with respect to the physical forward model is pivotal for reliably solving inverse problems. This consistency is mostly un-controlled in the current end-to-end deep learning methodologies proposed for the Magnetic Resonance Fingerprinting (MRF) problem. To address this, we propose ProxNet, a learned proximal gradient descent framework that directly incorporates the forward acquisition and Bloch dynamic models within a recurrent learning mechanism. The ProxNet adopts a compact neural proximal model for de-aliasing and quantitative inference, that can be flexibly t…
Recently, Magnetic Resonance Fingerprinting (MRF) was proposed as a quantitative imaging technique for the simultaneous acquisition of tissue parameters such as relaxation times $T_1$ and $T_2$. Although the acquisition is highly accelerated, the state-of-the-art reconstruction suffers from long computation times: Template matching methods are used to find the most similar signal to the measured one by comparing it to pre-simulated signals of possible parameter combinations in a discretized dictionary. Deep learning approaches can overcome this limitation, by providing the direct mapping from …
Leiden University Medical Center（莱顿大学医学中心）；Philips Research Hamburg（飞利浦汉堡研究院）；Delft University of Technology（代尔夫特理工大学）
In Magnetic Resonance Fingerprinting (MRF) the quality of the estimated parameter maps depends on the encoding capability of the variable flip angle train. In this work we show how the dimensionality reduction technique Hierarchical Stochastic Neighbor Embedding (HSNE) can be used to obtain insight into the encoding capability of different MRF sequences. Embedding high-dimensional MRF dictionaries into a lower-dimensional space and visualizing them with colors, being a surrogate for location in low-dimensional space, provides a comprehensive overview of particular dictionaries and, in addition…
Magnetic Resonance Fingerprinting (MRF) methods typically rely on dictionary matching to map the temporal MRF signals to quantitative tissue parameters. These methods suffer from heavy storage and computation requirements as the dictionary size grows. To address these issues, we proposed an end to end fully convolutional neural network for MRF reconstruction (MRF-FCNN), which firstly employ linear dimensionality reduction and then use neural network to project the data into the tissue parameters manifold space. Experiments on the MAGIC data demonstrate the effectiveness of the method.
University of Bern（伯尔尼大学）；Bern University Hospital（伯尔尼大学医院）；Institute of Myology（肌学研究所）；CEA（法国原子能与替代能源委员会）
Magnetic resonance fingerprinting (MRF) provides a unique concept for simultaneous and fast acquisition of multiple quantitative MR parameters. Despite acquisition efficiency, adoption of MRF into the clinics is hindered by its dictionary matching-based reconstruction, which is computationally demanding and lacks scalability. Here, we propose a convolutional neural network-based reconstruction, which enables both accurate and fast reconstruction of parametric maps, and is adaptable based on the needs of spatial regularization and the capacity for the reconstruction. We evaluated the method usi…
ARTORG Center for Biomedical Research, University of Bern（伯尔尼大学ARTORG生物医学研究中心）；Insel Data Science Center, Inselspital, Bern University Hospital（伯尔尼大学医院因塞尔spital因塞尔数据科学中心）；Institute of Myology, Neuromuscular Investigation Center, Paris（巴黎肌病研究所神经肌肉研究中心）；CEA, DRF, IBFJ, MIRCen, Paris（法国原子能和替代能源委员会DRF部门IBFJ分部MIRCen中心）
Magnetic resonance fingerprinting (MRF) enables fast and multiparametric MR imaging. Despite fast acquisition, the state-of-the-art reconstruction of MRF based on dictionary matching is slow and lacks scalability. To overcome these limitations, neural network (NN) approaches estimating MR parameters from fingerprints have been proposed recently. Here, we revisit NN-based MRF reconstruction to jointly learn the forward process from MR parameters to fingerprints and the backward process from fingerprints to MR parameters by leveraging invertible neural networks (INNs). As a proof-of-concept, we …
Magnetic Resonance Fingerprinting (MRF) enables the simultaneous quantification of multiple properties of biological tissues. It relies on a pseudo-random acquisition and the matching of acquired signal evolutions to a precomputed dictionary. However, the dictionary is not scalable to higher-parametric spaces, limiting MRF to the simultaneous mapping of only a small number of parameters (proton density, T1 and T2 in general). Inspired by diffusion-weighted SSFP imaging, we present a proof-of-concept of a novel MRF sequence with embedded diffusion-encoding gradients along all three axes to effi…
Magnetic Resonance Fingerprinting (MRF) is a novel technique that simultaneously estimates multiple tissue-related parameters, such as the longitudinal relaxation time T1, the transverse relaxation time T2, off resonance frequency B0 and proton density, from a scanned object in just tens of seconds. However, the MRF method suffers from aliasing artifacts because it significantly undersamples the k-space data. In this work, we propose a compressed sensing (CS) framework for simultaneously estimating multiple tissue-related parameters based on the MRF method. It is more robust to low sampling ra…
Mathematical models are becoming increasingly important in magnetic resonance imaging (MRI), as they provide a mechanistic approach for making a link between tissue microstructure and signals acquired using the medical imaging instrument. The Bloch equations, which describes spin and relaxation in a magnetic field, is a set of integer order differential equations with a solution exhibiting mono-exponential behaviour in time. Parameters of the model may be estimated using a non-linear solver, or by creating a dictionary of model parameters from which MRI signals are simulated and then matched w…
Adaptive Gate-Aware Mamba Networks for Magnetic Resonance Fingerprinting
School of Electrical Engineering and Computer Science, University of Queensland（电气工程与计算机科学学院，昆士兰大学）；School of Computer Science and Engineering, Central South University（计算机科学与工程学院，中南大学）；Image X Institute, Sydney School of Health Sciences, Faculty of Medicine and Health, University of Sydney（Image X研究所，悉尼健康科学学院，医学与健康学院，悉尼大学）；Donders Institute for Brain Cognition and Behaviour, Radboud University（脑认知与行为研究所，拉德堡德大学）；Australian Institute for Bioengineering and Nanotechnology, University of Queensland（生物工程与纳米技术研究所，昆士兰大学）；School of Engineering, University of Newcastle（工程学院，新castle大学）
Anomaly detection and localization are important problems in computer vision. Recently, Convolutional Neural Network (CNN) has been used for visual inspection. In particular, the scarcity of anomalous samples increases the difficulty of this task, and unsupervised leaning based methods are attracting attention. We focus on Student-Teacher Feature Pyramid Matching (STPM) which can be trained from only normal images with small number of epochs. Here we proposed a powerful method which compensates for the shortcomings of STPM. Proposed method consists of two students and two teachers that a pair …
Quantitative MRI methods that estimate multiple physical parameters simultaneously often require the fitting of a computational complex signal model defined through the Bloch equations. Repeated Bloch simulations can be avoided by matching the measured signal with a precomputed signal dictionary on a discrete parameter grid, as used in MR Fingerprinting. However, accurate estimation requires discretizing each parameter with a high resolution and consequently high computational and memory costs for dictionary generation, storage, and matching. Here, we reduce the required parameter resolution b…
Local feature matching is a computationally intensive task at the subpixel level. While detector-based methods coupled with feature descriptors struggle in low-texture scenes, CNN-based methods with a sequential extract-to-match pipeline, fail to make use of the matching capacity of the encoder and tend to overburden the decoder for matching. In contrast, we propose a novel hierarchical extract-and-match transformer, termed as MatchFormer. Inside each stage of the hierarchical encoder, we interleave self-attention for feature extraction and cross-attention for feature matching, yielding a huma…
We explore the application of concepts developed in High Energy Physics (HEP) for advanced medical data analysis. Our study case is a problem with high social impact: clinically-feasible Magnetic Resonance Fingerprinting (MRF). MRF is a new, quantitative, imaging technique that replaces multiple qualitative Magnetic Resonance Imaging (MRI) exams with a single, reproducible measurement for increased sensitivity and efficiency. A fast acquisition is followed by a pattern matching (PM) task, where signal responses are matched to entries from a dictionary of simulated, physically-feasible response…
