Deep Learning Fast MRI Using Channel Attention in Magnitude Domain

Super-resolution reconstruction of single anisotropic 3D MR images using residual convolutional neural network

Accelerating Magnetic Resonance Imaging (MRI) acquisition process is a critical and challenging medical imaging problem as basic reconstructions obtained from the undersampled k-space often exhibit blur or aliasing effects. Despite its significance and recent advancements in the field of deep neural networks (DNNs), development of deep learning-based MRI reconstruction algorithms is not yet flourished due to unavailability of public and large datasets. The recently introduced large-scale fastMRI dataset is posed to change this state of affairs, however, existing DNN solutions developed based on fastMRI require learning a large number of parameters rendering their practical application limited due to the strict low-latency requirements of real-time MRI acquisition. In this paper, we aim to address this drawback and target reducing the computational cost associated with single-coil reconstruction task. More specifically, the paper proposes a novel deep model referred to as the SepUnet architecture achieving significant reduction in the required number of parameters while maintaining high accuracy. Performance of the proposed SepUnet architecture is evaluated based on the official test dataset from fastMRI illustrating accuracy improvement in comparison to its published counterparts while requiring significantly reduced number of trainable parameters (i.e., the SepUnet architecture is much faster and lighter than its counterparts).

Artificial intelligence (AI) has the potential to fundamentally change radiology workflow. This review article provides an overview of AI applications in cardiovascular radiology with afocus on image acquisition, image reconstruction, and workflow optimization. First, established applications of AI are presented for cardiovascular computed tomography (CT) and magnetic resonance imaging (MRI). Building on this, we describe the range of applications that are currently being developed and evaluated. The practical benefits, opportunities, and potential risks of artificial intelligence in cardiovascular imaging are critically discussed. The presentation is based on the relevant specialist literature and our own clinical and scientific experience. AI-based techniques for image reconstruction are already commercially available and enable dose reduction in cardiovascular CT and accelerated image acquisition in cardiac MRI. Postprocessing of cardiovascular CT and MRI examinations can already be considerably simplified using established AI-based segmentation algorithms. In contrast, the practical benefits of many AI applications aimed at the diagnosis of cardiovascular diseases are less evident. Potential risks such as automation bias and considerations regarding cost efficiency should also be taken into account. In amarket characterized by great expectations and rapid technical development, it is important to realistically assess the practical benefits of AI applications for your own hospital or practice.

The deep learning method is an efficient solution for improving the quality of undersampled magnetic resonance (MR) image reconstruction while reducing lengthy data acquisition. Most deep learning methods neglect the mutual constraints between the real and imaginary components of complex-valued k-space data. In this paper, a new complex-valued convolutional neural network, namely, Dense-U-Dense Net (DUD-Net), is proposed to interpolate the undersampled k-space data and reconstruct MR images. The proposed network comprises dense layers, U-Net, and other dense layers in sequence. The dense layers are used to simulate the mutual constraints between real and imaginary components, and U-Net performs feature sparsity and interpolation estimation for k-space data. Two MRI datasets were used to evaluate the proposed method: brain magnitude-only MR images and knee complex-valued k-space data. Several operations were conducted for data preprocessing. First, the complex-valued MR images were synthesized by phase modulation on magnitude-only images. Second, a radial trajectory based on the golden angle was used for k-space undersampling, whereby a reversible normalization method was proposed to balance the distribution of positive and negative values in k-space data. The optimal performance of DUD-Net was demonstrated based on a quantitative evaluation of inter-method and intra-method comparisons. When compared with other methods, significant improvements were achieved, PSNRs were increased by 10.78 and 5.74dB, whereas RMSEs were decreased by 71.53% and 30.31% for magnitude and phase image, respectively. It is concluded that DUD-Net significantly improves the performance of MR image reconstruction.

Radial encoding is often performed for fast data acquisition in magnetic resonance imaging (MRI). Therefore, the gridding method, which is a kind of algorithm for Fast Fourier Transform, is widely used in fast MRI reconstruction. In this paper, an improved gridding method has been utilized to 2D MRI reconstruction, which precomputes an 1D finely sampled table of a high-accuracy interpolator and then uses separable bilinear interpolation by look-up table. Experimental comparisons are made by assessing the performance of the direct reconstruction, the conventional KB gridding and the proposed method. The experimental results show that the proposed method provides high accuracy, fast computation, and dramatic memory saving.

PBPK model of methotrexate in cerebrospinal fluid ventricles using a combined microdialysis and MRI acquisition

An understanding of data acquisition and processing in magnetic resonance imaging (MRI) facilitates subsequent manipulation and analysis of the resultant images. Unlike other medical imaging modalities, MRI is not well described in terms of the transmission and reception of a propagating wave since the wavelength of the radiofrequency signals involved is on the order of meters. Rather, MRI exploits the fact that the magnetization vectors associated with certain atoms (notably protons in water) will, when placed in a strong magnetic field, oscillate at a frequency proportional to that field. By spatially varying the magnetic field, position is mapped by the frequency and phase of the field effects caused by the oscillating magnetization vectors at each location. The data acquisition associated with this spatial mapping can be described as temporally scanning the Fourier or spatial frequency domain of the volume of interest. Image reconstruction is achieved by an inverse Fourier transform of the received signal. The Fourier representation of the imaging process is developed from an overview of the physics underlying MRI signal behaviour. Under this formalism, trade-offs in acquisition time, resolution, and field-of-view as well as image degradation associated with noise are addressed. Finally, the ability in MRI to manipulate soft tissue contrast over a wide range of independent parameters is outlined. >

In many in vivo magnetic resonance imaging (MRI) acquisitions, the image resolution is low and induces considerable segmentation errors with a poor and limited visual interpretation. Acquiring high-resolution images reduces the patient comfort and results in considerable cost because of an increase of the acquisition time. We developed a progressive technique based on multidimensional dual kriging to interpolate 2D and 3D multi-parametric MRI data. The objectives were to (1) optimise kriging parameters for 2D images and 3D volumes interpolation, (2) validate the technique in increasing the image resolution and (3) provide a direct application to 3D non-parametric volumes interpolation and image filtering. We carried out two multi-parametric MRI acquisitions on a bovine tail segment including intervertebral discs from the second to the fourth caudal vertebrae with two different spatial resolutions. We adopted the dual kriging formulation and introduced the technique of progressive kriging, which consists in kriging the given Cartesian data region-by-region. Kriging parameters were optimised to minimise the relative errors. For each MRI sequence, kriging was compared with other interpolation techniques in terms of signal mean within the region of interest, including the zero-padding, the nearest-neighbour, the bilinear and the bicubic techniques. Optimal kriging parameters for transverse relaxation time maps interpolation were a cubic covariance function and a distance of influence of only 1–8 pixels. Our technique was found to be efficient to interpolate the longitudinal and transverse relaxation times, the magnetisation transfer ratio and the apparent diffusion coefficient maps, compared with zero-padding, nearest-neighbour, bilinear and bicubic techniques. Kriging provided relatively high performance and low error, whereas image edges tend to be corrected and better defined compared with other techniques. Progressive dual kriging is a flexible technique that can be optimised to interpolate multidimensional data based on the signal distribution and should open doors to many future applications in medical imaging such as diffusion MRI, image filtering and non-parametric 3D volume reconstruction.

Mild traumatic brain injury (mTBI) sustained in early childhood affects the brain at a peak developmental period and may disrupt sensitive stages of skill acquisition, thereby compromising child functioning. However, due to the challenges of collecting non-sedated neuroimaging data in young children, the consequences of mTBI on young children's brains have not been systematically studied. In typically developing preschool children (of age 3-5years), a brief behavioral-play familiarization provides an effective alternative to sedation for acquiring awake magnetic resonance imaging (MRI) in a time- and resource-efficient manner. To date, no study has applied such an approach for acquiring non-sedated MRI in preschool children with mTBI who may present with additional MRI acquisition challenges such as agitation or anxiety. The present study aimed to compare the effectiveness of a brief behavioral-play familiarization for acquiring non-sedated MRI for research purposes between young children with and without mTBI, and to identify factors associated with successful MRI acquisition. Preschool children with mTBI (n=13) and typically developing children (n=24) underwent a 15-minutes behavioral-play MRI familiarization followed by a 35-minutes non-sedated MRI protocol. Success rate was compared between groups, MRI quality was assessed quantitatively, and factors predicting success were documented. Among the 37 participants, 15 typically developing children (63%) and 10 mTBI (77%) reached the MRI acquisition success criteria (i.e., completing the two first sequences). The success rate was not significantly different between groups (p=.48; 95% CI [-0.36 14.08]; Cramer's V=.15). The images acquired were of high-quality in 100% (for both groups) of the structural images, and 60% (for both groups) of the diffusion images. Factors associated with success included older child age (Β=0.73, p=.007, exp(B)=3.11, 95% CI [1.36 7.08]) and fewer parental concerns (Β=-1.56, p=.02, exp(Β)=0.21, 95% CI [0.05 0.82]) about the MRI procedure. Using brief behavioral-play familiarization allows acquisition of high-quality non-sedated MRI in young children with mTBI with success rates comparable to those of non-injured peers.

Recently, magnetic resonance imaging (MRI) has become a crucial medical imaging technology widely used in clinical practice. However, MRI faces challenges such as the lengthy acquisition time for k-space data and the need for time-consuming manual annotation by radiologists. Traditionally, these challenges have been addressed individually through undersampled MRI reconstruction and automatic segmentation algorithms. Whether undersampled MRI segmentation can be enhanced by treating undersampled MRI reconstruction and segmentation as an end-to-end task, trained simultaneously, rather than as serial tasks should beexplored. We introduce a novel Transformer- and Joint Learning-based Dual-domain Network (TJLD-Net) for undersampled MRIsegmentation. This method significantly enhances feature recognition in the segmentation process by fully utilizing the rich detail obtained during the image reconstruction phase. Consequently, the method can achieve precise and reliable image segmentation even with undersampled k-space data. Additionally, it incorporates an attention mechanism for feature enhancement, which improves the representation of shared features by learning the contextual information in MRimages. Simulation experiments demonstrate that the segmentation performance of TJLD-Net on three datasets is significantly higher than that of the joint model (RecSeg) and six baseline models (where reconstruction and segmentation are regarded as serial tasks). On the CHAOS dataset, the Dice scores of TJLD-Net are, on average, 9.87%, 2.17%, 1.90%, 1.80%, 9.60%, 0.80%, and 6.50% higher than those of the seven compared models. On the ATLAS challenge dataset, the average Dice scores of TJLD-Net improve by 4.23%, 5.63%, 2.30%, 1.53%, 3.57%, 0.93%, and 6.60%. Similarly, on the SKM-TEA dataset, the average Dice scores of TJLD-Net improve by 4.73%, 12.80%, 14.83%, 8.67%, 4.53%, 11.60%, and 12.10%. The novel TJLD-Net model provides a promising solution for undersampled MRI segmentation, overcoming the poor performance issues encountered by automated segmentation algorithms in low-quality acceleratedimaging.

Dynamic magnetic resonance imaging (MRI) has been extensively utilized for enhancing medical living environment visualization, however, in clinical practice it often suffers from long data acquisition times. Dynamic imaging essentially reconstructs the visual image from raw (k,t)-space measurements, commonly referred to as big data. The purpose of this work is to accelerate big medical data acquisition in dynamic MRI by developing a non-convex minimization framework. In particular, to overcome the inherent speed limitation, both non-convex low-rank and sparsity constraints were combined to accelerate the dynamic imaging. However, the non-convex constraints make the dynamic reconstruction problem difficult to directly solve through the commonly-used numerical methods. To guarantee solution efficiency and stability, a numerical algorithm based on Alternating Direction Method of Multipliers (ADMM) is proposed to solve the resulting non-convex optimization problem. ADMM decomposes the original complex optimization problem into several simple sub-problems. Each sub-problem has a closed-form solution or could be efficiently solved using existing numerical methods. It has been proven that the quality of images reconstructed from fewer measurements can be significantly improved using non-convex minimization. Numerous experiments have been conducted on two in vivo cardiac datasets to compare the proposed method with several state-of-the-art imaging methods. Experimental results illustrated that the proposed method could guarantee the superior imaging performance in terms of quantitative and visual image quality assessments.

Compressed sensing (CS) is extensively used to reduce magnetic resonance imaging (MRI) acquisition time. State-of-the-art deep learning-based methods have proven effective in obtaining fast, high-quality reconstruction of CS-MR images. However, they treat the inherently complex-valued MRI data as real-valued entities by extracting the magnitude content or concatenating the complex-valued data as two real-valued channels for processing. In both cases, the phase content is discarded. To address the fundamental problem of real-valued deep networks, i.e. their inability to process complex-valued data, we propose a complex-valued generative adversarial network (Co-VeGAN) framework, which is the first-of-its-kind generative model exploring the use of complex-valued weights and operations. Further, since real-valued activation functions do not generalize well to the complex-valued space, we propose a novel complex-valued activation function that is sensitive to the input phase and has a learnable profile. Extensive evaluation of the proposed approach <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> on different datasets demonstrates that it significantly outperforms the existing CS-MRI reconstruction techniques.

Accelerating the acquisition of magnetic resonance imaging (MRI) is a challenging problem, and many works have been proposed to reconstruct images from undersampled k-space data. However, if the main purpose is to extract certain quantitative measures from the images, perfect reconstructions may not always be necessary as long as the images enable the means of extracting the clinically relevant measures. In this paper, we work on jointly predicting cardiac motion estimation and segmentation directly from undersampled data, which are two important steps in quantitatively assessing cardiac function and diagnosing cardiovascular diseases. In particular, a unified model consisting of both motion estimation branch and segmentation branch is learned by optimising the two tasks simultaneously. Additional corresponding fully-sampled images are incorporated into the network as a parallel sub-network to enhance and guide the learning during the training process. Experimental results using cardiac MR images from 220 subjects show that the proposed model is robust to undersampled data and is capable of predicting results that are close to that from fully-sampled ones, while bypassing the usual image reconstruction stage.

The possibility to perform an early and repeatable assessment of imaging performance is fundamental in the design and development process of new ultrasound (US) probes. Particularly, a more realistic analysis with application-specific imaging targets can be extremely valuable to assess the expected performance of US probes in their potential clinical field of application. The experimental protocol presented in this work was purposely designed to provide an application-specific assessment procedure for newly-developed US probe prototypes based on Capacitive Micromachined Ultrasonic Transducer (CMUT) technology in relation to brain imaging. The protocol combines the use of a bovine brain fixed in formalin as the imaging target, which ensures both realism and repeatability of the described procedures, and of neuronavigation techniques borrowed from neurosurgery. The US probe is in fact connected to a motion tracking system which acquires position data and enables the superposition of US images to reference Magnetic Resonance (MR) images of the brain. This provides a means for human experts to perform a visual qualitative assessment of the US probe imaging performance and to compare acquisitions made with different probes. Moreover, the protocol relies on the use of a complete and open research and development system for US image acquisition, i.e. the Ultrasound Advanced Open Platform (ULA-OP) scanner. The manuscript describes in detail the instruments and procedures involved in the protocol, in particular forthe calibration, image acquisition and registration of US and MR images. The obtained results prove the effectiveness of the overall protocol presented, which is entirely open (within the limits of the instrumentation involved), repeatable, and covers the entire set of acquisition and processing activities for US images.

Nuclear magnetic resonance imaging (MRI) has become the gold standard for many imaging applications. It is routinely used to detect diseases and tissue pathologies due to its superior soft tissue contrast and high spatial resolution. Unlike other imaging techniques such as X-rays, computed tomography, it does not harm patients with ionising radiation.However, MRIs are expensive and only a small portion of patients who would benefit from them can access them. The pursuit of higher sensitivity has generated a trend towards increasing the already large static magnetic field. This has improved imaging quality but has made this technology more expensive and further hindered MRI accessibility. The main cost driver of MRI machines is the strong magnet.The collection of techniques being developed to overcome the intrinsic low NMR sensitivity has fostered interest in low field (LF) MRI to improve cost-effectiveness of MRI. First, the purchase and operational cost of LF systems is relatively low. Second, they are more compatible with other instrumentation which enables versatile concepts such as application-specific open systems and intraoperative imaging. LF systems can offer a wide range of configurations by using permanent magnets. Third, the small fringe field lowers the risk to patients and workers and makes the magnet easier to site. Fourth, artefacts which rely on the strength of field are reduced, as well as the specific absorption rate (SAR) in tissues.Ultra-low field (ULF) MRI systems employ field strengths lower than 10 mT. These systems can complement the advantages of LF systems mentioned above with additional potential benefits. The requirement of homogeneity in ULF is relaxed extensively. It is possible to adjust the strength and direction of the measurement field, allowing flexibility in pulse sequences. Moreover, ULF systems operate in the low kHz frequency range, avoiding the need for radio frequency (RF) noise shielding and enhancing T1-weighted contrast.Most ULF MRI research concentrates on using expensive and fragile sensors, produces the magnetic fields through resistive coils and employs linear gradient fields for encoding. Although ULF systems are important low-cost and portable MRI candidates, they still need considerable space to generate linear fields and need expensive and bulky high permeability shielding to suppress ambient noise.This PhD project develops two major solutions towards a portable and low-cost ULF MRI system: a software gradiometer based on machine learning for ambient noise cancellation and a fast iterative algorithm with total variation (TV) regularisation for image reconstruction. In addition, a concept for a dynamical permanent magnet array (PMA) ULF MRI system is proposed with nonlinear 3D spatial encoding.First, I introduce an experimental setup as a platform for evaluating the MR signal in the ULF regime using a Helmholtz coil as a framework. It is composed of a measurement field, an NMR console, a transmit and receive coil, and a shielding box. The NMR signal is successfully acquired and analysed in partial shielding and full shielding. The results suggest that partial shielding of ULF MRI instruments has the potential to generate a strong signal. This system is built for a subsequent study on noise cancellation presented in following chapter.The second study is a convolutional neural network (CNN) based software gradiometer for background noise cancellation. It includes three ambient noise monitoring coils which are placed away from the NMR sensing coil. The noise induced in the sensing coils is estimated using machine learning. The results show that the software gradiometer reduces ambient noise and can be used to relax shielding requirements, thereby reducing the size and weight of the shielding box.The concept of using small magnets for 3D-spatial encoding in dynamical PMA based ULF MRI is described. It uses small rectangular permanent magnets to generate a 3D-spatial encoding field. The encoding magnets move along an optimised trajectory to achieve an encoding matrix with a low condition number. A prototype of the 3D-spatial encoding has been built and its feasibility tested. The described encoding system can reduce the volume and energy requirements and improve the portability of ULF MRI systems.Finally, iterative imaging reconstruction algorithms for ULF MR are studied. The current state-of-the-art methods are evaluated, which includes Simultaneous Iterative Reconstruction Technique (ART/SIRT), Conjugate Gradient Least Squares (CGLS), and the Chambolle-Pock (CP) algorithms. A dynamic weight Column Action Reconstruction Technique (dwCART) method is proposed and applied to image reconstruction with TV regularisation in the setting of undersampling. In the absence of having a finalised prototype to acquire real ULF MRI imaging data, the methods are tested on CT models (using both simulated and real CT data). The dwCART algorithm performed best on the tested CT problems. It paves the way for fast and accurate imaging with the PMA-based ULF MRI system.