Discovering a new field is not usually an easy process, especially when you choose magnetic resonance imaging (MRI). MRI is one of the few non-invasive medical procedures, if not the only one, that someone can receive in modern day hospitals. Its high sensitivity is a true prowess that is due to three things: subtle quantum physics, great engineering and clever imaging techniques from mathematics and computing science. However, the mathematics and physics of it are already daunting tasks by themselves, which makes MRI difficult to comprehend. This document paves a rather short, yet solid and logical, path from the subtle concept of spin to the current limitations of diffusion MRI. It then describes more advanced encoding methods designed to overcome diffusion MRI's limitations, such as tensor-valued encoding.
Cross-term spatiotemporal encoding (xSPEN) is a recently introduced imaging approach delivering single-scan 2D NMR images with unprecedented resilience to field inhomogeneities. The method relies on performing a pre-acquisition encoding and a subsequent image read out while using the disturbing frequency inhomogeneities as part of the image formation processes, rather than as artifacts to be overwhelmed by the application of external gradients. This study introduces the use of this new single-shot MRI technique as a diffusion-monitoring tool, for accessing regions that have hitherto been unapp…
Diffusion encoding along multiple spatial directions per signal acquisition can be described in terms of a b-tensor. The benefit of tensor-valued diffusion encoding is that it unlocks the "shape of the b-tensor" as a new encoding dimension. By modulating the b-tensor shape, we can control the sensitivity to microscopic diffusion anisotropy which can be used as a contrast mechanism; a feature that is inaccessible by conventional diffusion encoding. Since imaging methods based on tensor-valued diffusion encoding are finding an increasing number of applications we are prompted to highlight the ch…
Multi-dimensional non-Cartesian MRI encoding using the precomputed interpolator can encounter the curse of dimensionality, in which the interpolator size exceeds the available memory on the parallel accelerators. Here we reformulate the multi-dimensional non-uniform fast Fourier transform (NUFFT) to a tensor form. The exponentially growing size of the fully precomputed interpolator can be reduced by tensor analysis. We propose a tree-like, mixed-radix tensor method which flexibly reduces the storage of the NUFFT. A parallel tensor product algorithm is proposed and tested with in vivo cardiac M…
Monash University（莫纳什大学）；Indian Institute of Technology Bombay（印度理工学院孟买分校）；IITB Monash Research Academy（IITB-莫纳什研究学院）；Swinburne University of Technology（斯威本科技大学）
The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP) of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS). In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are max…
Purpose: Eddy currents might lead to image distortions in diffusion weighted echo planar imaging. A method is proposed to reduce their effects on double diffusion encoding (DDE) MRI experiments and the thereby derived microscopic fractional anisotropy (μFA) . Methods: The twice refocused spin echo scheme was adapted for DDE measurements. To assess the effect of individual diffusion encodings on the image distortions, measurements of a grid of plastic rods in water were performed. The effect of eddy current compensation on μFA measurements was evaluated in the brains of six healthy volunteers. …
Purpose: Microscopic fractional anisotropy (μFA) can disentangle microstructural information from orientation dispersion. While double diffusion encoding (DDE) MRI methods are widely used to extract accurate μFA, it has only recently been proposed that powder-averaged single diffusion encoding (SDE) signals, when coupled with the diffusion standard model (SM) and a set of constraints, could be used for μFA estimation. This study aims to evaluate μFA as derived from the spherical mean technique (SMT) set of constraints, as well as more generally for powder-averaged SM signals. Methods: SDE expe…
University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Korea University（高丽大学）
Diffusion MRI (dMRI) is a unique imaging technique for in vivo characterization of tissue microstructure and white matter pathways. However, its relatively long acquisition time implies greater motion artifacts when imaging, for example, infants and Parkinson's disease patients. To accelerate dMRI acquisition, we propose in this paper (i) a diffusion encoding scheme, called Slice-Interleaved Diffusion Encoding (SIDE), that interleaves each diffusion-weighted (DW) image volume with slices that are encoded with different diffusion gradients, essentially allowing the slice-undersampling of image …
Purpose: Biophysical tissue models are increasingly used in the interpretation of diffusion MRI (dMRI) data, with the potential to provide specific biomarkers of brain microstructural changes. However, the general Standard Model has recently shown that model parameter estimation from dMRI data is ill-posed unless very strong magnetic gradients are used. We analyse this issue for the Neurite Orientation Dispersion and Density Imaging with Diffusivity Assessment (NODDIDA) model and demonstrate that its extension from Single Diffusion Encoding (SDE) to Double Diffusion Encoding (DDE) solves the i…
Purpose: To assess the technical feasibility of whole-brain diffusional variance decomposition (DIVIDE) based on q-space trajectory encoding (QTE) at clinical MRI systems with varying performance. DIVIDE is used to separate diffusional heterogeneity into components that arise due to isotropic and anisotropic tissue structures. Methods: We designed imaging protocols for DIVIDE using numerically optimized gradient waveforms for diffusion encoding. Imaging was performed at systems with magnetic field strengths between 1.5 and 7 T, and gradient amplitudes between 33 and 80 mT/m. Technical feasibil…
Purpose: Double diffusion encoding (DDE) MRI enables the estimation of microscopic diffusion anisotropy, yielding valuable information on tissue microstructure. A recent study proposed that the acquisition of rotationally invariant DDE metrics, typically obtained using a spherical "5-design", could be greatly simplified by assuming Gaussian diffusion, facilitating reduced acquisition times that are more compatible with clinical settings. Here, we aim to validate the new minimal acquisition scheme against the standard DDE 5-design, and to quantify the proposed method's noise robustness to facil…
Purpose: To enable rigid-body motion tolerant parallel volumetric magnetic resonance imaging by retrospective head motion correction on a variety of spatio-temporal scales and imaging sequences. Theory and methods: Tolerance against rigid-body motion is based on distributed and incoherent sampling orders for boosting a joint retrospective motion estimation and reconstruction framework. Motion resilience stems from the encoding redundancy in the data, as generally provided by the coil array. Hence, it does not require external sensors, navigators or training data, so the methodology is readily …
Heart failure is a leading cause of mortality in the Western world. The mouse is a widely used model for a number of diseases, induced by genetic modification or surgical intervention. When performing experiments in mice, in vivo magnetic resonance imaging (MRI) can be used to evaluate heart anatomy and function at multiple levels. Volumetric measurements of ventricle size at each phase of the heart cycle (obtained with cine MRI) can be used as a sensitive measure for heart failure. Cine MRI is applied here to genetic models of heart disease, including stress tests with pharmacological manipul…
We enable the estimation of the per-axon axial diffusivity from single encoding, strongly diffusion-weighted, pulsed gradient spin echo data. Additionally, we improve the estimation of the per-axon radial diffusivity compared to estimates based on spherical averaging. The use of strong diffusion weightings in magnetic resonance imaging (MRI) allows to approximate the signal in white matter as the sum of the contributions from axons. At the same time, spherical averaging leads to a major simplification of the modeling by removing the need to explicitly account for the unknown orientation distri…
High-fidelity 3D multi-slab diffusion MRI using Slab-shifting for Harmonized 3D Acquisition and Reconstruction with Profile Encoding Networks (SHARPEN)
Diffusion-weighted MRI (DW-MRI) has recently seen a rising interest in planar, spherical and general B-tensor encodings. Some of these sequences have aided traditional linear encoding in the estimation of white matter microstructural features, generally by making DW-MRI less sensitive to the orientation of axon fascicles in a voxel. However, less is known about their potential to make the signal more sensitive to fascicle orientation, especially in crossing-fascicle voxels. Although planar encoding has been commended for the resemblance of its signal with the voxel's orientation distribution f…
We propose a radical advance in Magnetic Resonance Imaging. MRI remains slow because it requires successive applications of magnetic field gradients to encode for spatial location. Parallel MRI accelerates imaging by permitting undersampling of k-space using multiple detectors, each with a unique spatial sensitivity to the radio field emitted by the object. This is called spatial sensitivity encoding. A fourfold undersampling means a fourfold acceleration, however a five-fold undersampling cannot be reconstructed. This is because too much reliance is placed on spatial sensitivity encoding, and…
Purpose: To evaluate the feasibility of a 3-minute b-tensor encoding protocol for diffusion MRI-based assessment of the microscopic anisotropy and tissue heterogeneity in a wide range of intracranial tumors. Methods: B-tensor encoding was performed in 42 patients with intracranial tumors (gliomas, meningiomas, adenomas, metastases). Microscopic anisotropy and tissue heterogeneity were evaluated by estimating the anisotropic kurtosis ($MK_A$) and isotropic kurtosis ($MK_I$), respectively. An extensive imaging protocol was compared with a faster 3-minute protocol. Results: The fast imaging proto…
ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging
Amsterdam University Medical Center（阿姆斯特丹大学医学中心）；University of Amsterdam（阿姆斯特丹大学）；Amsterdam Neuroscience（阿姆斯特丹神经科学研究所）；Informatics Institute, University of Amsterdam（阿姆斯特丹大学信息学研究所）
Multi-shot echo planar imaging (msEPI) is a promising approach to achieve high in-plane resolution with high sampling efficiency and low T2* blurring. However, due to the geometric distortion, shot-to-shot phase variations and potential subject motion, msEPI continues to be a challenge in MRI. In this work, we introduce acquisition and reconstruction strategies for robust, high-quality msEPI without phase navigators. We propose Blip Up-Down Acquisition (BUDA) using interleaved blip-up and -down phase encoding, and incorporate B0 forward-modeling into Hankel structured low-rank model to enable …
Purpose: To develop an efficient simultaneous multi-slab imaging method with blipped-controlled aliasing in parallel imaging (blipped-SMSlab) in a 4D k-space framework, and demonstrate its efficacy in high-resolution diffusion MRI (dMRI). Theory and Methods: First, the SMSlab 4D k-space signal expression is formulated, and the phase interferences from intra-slab and inter-slab encodings on the same physical z axis are analyzed. Then, the blipped-SMSlab dMRI sequence is designed, with blipped-CAIPI gradients for inter-slab encoding, and a 2D multi-band accelerated navigator for inter-kz-shot ph…
A model-based reconstruction technique for accelerated T2 mapping with improved accuracy is proposed using undersampled Cartesian spin-echo MRI data. The technique employs an advanced signal model for T2 relaxation that accounts for contributions from indirect echoes in a train of multiple spin echoes. An iterative solution of the nonlinear inverse reconstruction problem directly estimates spin-density and T2 maps from undersampled raw data. The algorithm is validated for simulated data as well as phantom and human brain MRI at 3 T. The performance of the advanced model is compared to conventi…
Multi-echo Chemical Shift Encoded methods for Fat-Water quantification are growing in clinical use due to their ability to estimate and correct some confounding effects. State of the art CSE water-fat separation approaches rely on a multi-peak fat spectrum with peak frequencies and relative amplitudes kept constant over the entire MRI dataset. However, the latter approximation introduces a systematic error in fat percentage quantification in patients where the differences in lipid chemical composition are significant, such as for neuromuscular disorders, because of the spatial dependence of th…
A Review of Electromagnetic Elimination Methods for low-field portable MRI scanner
Harvard Medical School（哈佛医学院）；University of Michigan（密歇根大学）；Harvard University（哈佛大学）；New York University（纽约大学）；Columbia University（哥伦比亚大学）；Guangxi University（广西大学）
Purpose: The expanded encoding model incorporates spatially- and time-varying field perturbations for correction during reconstruction. So far, these reconstructions have used the conjugate gradient method with early stopping used as implicit regularization. However, this approach is likely suboptimal for low-SNR cases like diffusion or high-resolution MRI. Here, we investigate the extent that l1-wavelet regularization, or equivalently compressed sensing (CS), combined with expanded encoding improves trade-offs between spatial resolution, readout time and SNR for single-shot spiral diffusion-w…
Portable low-cost MRI systems have the potential to enable point-of-care and timely MRI diagnosis, and to make this imaging modality available to routine scans and to underdeveloped areas. With simplicity, no maintenance, no power consumption, and low cost, permanent magnets or arrays are attractive to use as a source of magnetic field to realize portability and low cost for a scanners. However, when taking the Fourier imaging approach and using linear gradient fields, homogeneous fields are required, thus either a bulky magnet is needed, or the imaging volume is too small to image an organ if…
The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium such as brain tissue can be modeled by the Bloch-Torrey partial differential equation. The spatial integral of the solution of this equation in realistic geometry provides a gold-standard reference model for the diffusion MRI signal arising from different tissue micro-structures of interest. A closed form representation of this reference diffusion MRI signal has been derived twenty years ago, called Matrix Formalism that makes explicit the link between the La…
BART Streams: Real-time Reconstruction Using a Modular Framework for Pipeline Processing
Graz University of Technology（格拉茨工业大学）；Institute of Biomedical Imaging, Graz University of Technology（格拉茨工业大学生物医学成像研究所）；University Medical Center Göttingen（哥廷根大学医学中心）；Institute for Diagnostic and Interventional Radiology, University Medical Center Göttingen（哥廷根大学医学中心诊断与介入放射学研究所）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；German Centre for Cardiovascular Research (DZHK)（德国心血管研究中心）；BioTechMed-Graz（BioTechMed格拉茨）
Our objective is the calibration of mathematical tumor growth models from a single multiparametric scan. The target problem is the analysis of preoperative Glioblastoma (GBM) scans. To this end, we present a fully automatic tumor-growth calibration methodology that integrates a single-species reaction-diffusion partial differential equation (PDE) model for tumor progression with multiparametric Magnetic Resonance Imaging (mpMRI) scans to robustly extract patient specific biomarkers i.e., estimates for (i) the tumor cell proliferation rate, (ii) the tumor cell migration rate, and (iii) the orig…
Fiber-Resolved Microstructure Quantification from Multi-Shell Diffusion MRI using Detection Transformers
AImotion Bavaria, Technische Hochschule Ingolstadt（AImotion Bavaria，英戈尔施塔特应用技术大学）；TUM School of Computation, Information and Technology, Technical University of Munich（慕尼黑工业大学计算、信息与技术学院）；TUM School of Natural Sciences, Technical University of Munich（慕尼黑工业大学自然科学学院）
Real-time, inline quantitative MRI enabled by scanner-integrated machine learning: a proof of principle with NODDI
Hawkes Institute, Department of Computer Science, UCL（伦敦大学学院霍克斯研究所计算机科学系）；NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, Faculty of Brain Sciences, UCL（伦敦大学学院脑科学学院神经炎症系女王广场多发性硬化中心核磁共振研究单元）；Research and Collaborations GBI, Siemens Healthcare Ltd（西门子医疗有限公司研究与协作GBI部门）；Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust（伦敦大学学院医院NHS基金会信托国家神经病学和神经外科医院Lysholm神经放射科）；Neuroradiological Academic Unit, Dept of Translational Neuroscience and Stroke, UCL Queen Square Institute of Neurology, UCL（伦敦大学学院女王广场神经学研究所转化神经科学与卒中系神经放射学学术单元）；Centre for Cardiovascular Imaging, Institute of Cardiovascular Science, UCL（伦敦大学学院心血管科学研究所心血管成像中心）；Department of Brain & Behavioural Sciences, University of Pavia（帕维亚大学脑与行为科学系）；Digital Neuroscience Centre, IRCCS Mondino Foundation（IRCCS蒙迪诺基金会数字神经科学中心）
University of Waterloo（滑铁卢大学）；University of Toronto（多伦多大学）；Sunnybrook Research Institute（桑尼布鲁克研究所）
Magnetic Resonance Imaging (MRI) is a crucial medical imaging technology for the screening and diagnosis of frequently occurring cancers. However image quality may suffer by long acquisition times for MRIs due to patient motion, as well as result in great patient discomfort. Reducing MRI acquisition time can reduce patient discomfort and as a result reduces motion artifacts from the acquisition process. Compressive sensing strategies, when applied to MRI, have been demonstrated to be effective at decreasing acquisition times significantly by sparsely sampling the \emph{k}-space during the acqu…
One of the challenges in functional brain imaging is integration of complementary imaging modalities, such as magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive superconducting quantum interference devices (SQUIDs) to directly measure magnetic fields of neuronal currents, cannot be combined with conventional high-field MRI in a single instrument. Indirect matching of MEG and MRI data leads to significant co-registration errors. A recently proposed imaging method - SQUID-based microtesla MRI - can be naturally combined with MEG in the…
The Bloch equation describes the evolution of classical particles tagged with a magnetisation vector in a strong magnetic field and is fundamental to many NMR and MRI contrast methods. The equation can be generalised to include the effects of spin motion by including a spin flux, which typically contains a Fickian diffusive term and/or a coherent velocity term. This form is known as the Bloch-Torrey equation, and is fundamental to MR modalities which are sensitive to spin dynamics such as diffusion MRI. Such modalities have received a great deal of interest in the research literature over the …
Direct imaging of impressed dc currents inside the head can provide valuable conductivity information, possibly improving electro-magnetic neuroimaging. Ultra-low field magnetic resonance imaging (ULF MRI) at $μ$T Larmor fields can be utilized for current density imaging (CDI). Here, a measurable impact of the magnetic field $B_{J}$, generated by the impressed current density $J$, on the MR signal is probed using specialized sequences. In contrast to high-field MRI, the full tensor of $B_{J}$ can be derived without rotation of the subject in the scanner, due to a larger flexibility in the sequ…
Diffusion weighted imaging techniques permit us to infer microstructural detail in biological tissue in vivo and noninvasively. Modern sequences are based on advanced diffusion encoding schemes, allowing probing of more revealing measures of tissue microstructure than the standard apparent diffusion coefficient or fractional anisotropy. Though these methods may result in faster or more revealing acquisitions, they generally demand prior knowledge of sequence-specific parameters for which there is no accepted sharing standard. Here, we present a metadata labelling scheme suitable for the needs …
Massachusetts Institute of Technology（麻省理工学院）；École Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）；Athinoula A. Martinos Center for Biomedical Imaging（阿西努拉·A·马蒂诺斯生物医学成像中心）；Tsinghua University（清华大学）；Harvard Medical School（哈佛医学院）
Purpose: To develop a scan-specific model that estimates and corrects k-space errors made when reconstructing accelerated Magnetic Resonance Imaging (MRI) data. Methods: Scan-Specific Artifact Reduction in k-space (SPARK) trains a convolutional-neural-network to estimate and correct k-space errors made by an input reconstruction technique by back-propagating from the mean-squared-error loss between an auto-calibration signal (ACS) and the input technique's reconstructed ACS. First, SPARK is applied to GRAPPA and demonstrates improved robustness over other scan-specific models, such as RAKI and…
We present a design and the optimization of an irregular-shaped ring-pair magnet array that generates a 1D monotonic field pattern for 2D head imaging in a low-field portable MRI system. The magnet rings are discretized into fan-shaped ring segments with varying outer diameters for the design and optimization. Besides, the inner radii of ring-pairs are tapered from outside in to provide the controlled field inhomogeneity. Genetic algorithm (GA) was used, and a current model for a fan-shaped ring segment was derived to have a fast forward calculation in the optimization. A monotonic field patte…
Parallel imaging techniques have been widely used in high-field magnetic resonance imaging (MRI). Multiple receiver coils have been shown to improve image quality and allow accelerated image acquisition. Magnetic resonance imaging at ultra-low fields (ULF MRI) is a new imaging approach that uses SQUID (superconducting quantum interference device) sensors to measure the spatially encoded precession of pre-polarized nuclear spin populations at microtesla-range measurement fields. In this work, parallel imaging at microtesla fields is systematically studied for the first time. A seven-channel SQU…
Magnetic Resonance Imaging (MRI) of hard biological tissues is challenging due to the fleeting lifetime and low strength of their response to resonant stimuli, especially at low magnetic fields. Consequently, the impact of MRI on some medical applications, such as dentistry, continues to be limited. Here, we present three-dimensional reconstructions of ex-vivo human teeth, as well as a rabbit head and part of a cow femur, all obtained at a field strength of only 260 mT. These images are the first featuring soft and hard tissues simultaneously at sub-Tesla fields, and they have been acquired in…
University College London（伦敦大学学院）；University of Oulu（奥卢大学）
Magnetic Resonance Imaging (MRI) plays a vital role in diagnosis, management and monitoring of many diseases. However, it is an inherently slow imaging technique. Over the last 20 years, parallel imaging, temporal encoding and compressed sensing have enabled substantial speed-ups in the acquisition of MRI data, by accurately recovering missing lines of k-space data. However, clinical uptake of vastly accelerated acquisitions has been limited, in particular in compressed sensing, due to the time-consuming nature of the reconstructions and unnatural looking images. Following the success of machi…
