Undersampled Magnetic Resonance Imaging Research Articles

Fourier Convolution Block with global receptive field for MRI reconstruction

Reconstructing images from under-sampled Magnetic Resonance Imaging (MRI) signals significantly reduces scan time and improves clinical practice. However, Convolutional Neural Network (CNN)-based methods, while demonstrating great performance in MRI reconstruction, may face limitations due to their restricted receptive field (RF), hindering the capture of global features. This is particularly crucial for reconstruction, as aliasing artifacts are distributed globally. Recent advancements in Vision Transformers have further emphasized the significance of a large RF. In this study, we proposed a novel global Fourier Convolution Block (FCB) with whole image RF and low computational complexity by transforming the regular spatial domain convolutions into frequency domain. Visualizations of the effective RF and trained kernels demonstrated that FCB improves the RF of reconstruction models in practice. The proposed FCB was evaluated on four popular CNN architectures using brain and knee MRI datasets. Models with FCB achieved superior PSNR and SSIM than baseline models and exhibited more details and texture recovery. The code is publicly available at https://github.com/Haozhoong/FCB.

Transformer- and joint learning-based dual-domain networks for undersampled MRI segmentation.

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.

Task-based assessment for neural networks: evaluating undersampled MRI reconstructions based on human observer signal detection.

Recent research explores using neural networks to reconstruct undersampled magnetic resonance imaging. Because of the complexity of the artifacts in the reconstructed images, there is a need to develop task-based approaches to image quality. We compared conventional global quantitative metrics to evaluate image quality in undersampled images generated by a neural network with human observer performance in a detection task. The purpose is to study which acceleration (2×, 3×, 4×, 5×) would be chosen with the conventional metrics and compare it to the acceleration chosen by human observer performance. We used common global metrics for evaluating image quality: the normalized root mean squared error (NRMSE) and structural similarity (SSIM). These metrics are compared with a measure of image quality that incorporates a subtle signal for a specific task to allow for image quality assessment that locally evaluates the effect of undersampling on a signal. We used a U-Net to reconstruct under-sampled images with 2×, 3×, 4×, and 5× one-dimensional undersampling rates. Cross-validation was performed for a 500- and a 4000-image training set with both SSIM and MSE losses. A two-alternative forced choice (2-AFC) observer study was carried out for detecting a subtle signal (small blurred disk) from images with the 4000-image training set. We found that for both loss functions, the human observer performance on the 2-AFC studies led to a choice of a 2× undersampling, but the SSIM and NRMSE led to a choice of a 3× undersampling. For this detection task using a subtle small signal at the edge of detectability, SSIM and NRMSE led to an overestimate of the achievable undersampling using a U-Net before a steep loss of image quality between 2×, 3×, 4×, 5× undersampling rates when compared to the performance of human observers in the detection task.

Radial Undersampled MRI Reconstruction Using Deep Learning With Mutual Constraints Between Real and Imaginary Components of K-Space.

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.

Fourier Domain Robust Denoising Decomposition and Adaptive Patch MRI Reconstruction.

The sparsity of the Fourier transform domain has been applied to magnetic resonance imaging (MRI) reconstruction in k -space. Although unsupervised adaptive patch optimization methods have shown promise compared to data-driven-based supervised methods, the following challenges exist in MRI reconstruction: 1) in previous k -space MRI reconstruction tasks, MRI with noise interference in the acquisition process is rarely considered. 2) Differences in transform domains should be resolved to achieve the high-quality reconstruction of low undersampled MRI data. 3) Robust patch dictionary learning problems are usually nonconvex and NP-hard, and alternate minimization methods are often computationally expensive. In this article, we propose a method for Fourier domain robust denoising decomposition and adaptive patch MRI reconstruction (DDAPR). DDAPR is a two-step optimization method for MRI reconstruction in the presence of noise and low undersampled data. It includes the low-rank and sparse denoising reconstruction model (LSDRM) and the robust dictionary learning reconstruction model (RDLRM). In the first step, we propose LSDRM for different domains. For the optimization solution, the proximal gradient method is used to optimize LSDRM by singular value decomposition and soft threshold algorithms. In the second step, we propose RDLRM, which is an effective adaptive patch method by introducing a low-rank and sparse penalty adaptive patch dictionary and using a sparse rank-one matrix to approximate the undersampled data. Then, the block coordinate descent (BCD) method is used to optimize the variables. The BCD optimization process involves valid closed-form solutions. Extensive numerical experiments show that the proposed method has a better performance than previous methods in image reconstruction based on compressed sensing or deep learning.

DLGAN: Undersampled MRI reconstruction using Deep Learning based Generative Adversarial Network

Magnetic Resonance Imaging (MRI) is a crucial tool for quantitative image analysis and clinical diagnosis, providing detailed anatomical images to assist in the detection of various abnormalities. However, the widespread use of MRI is hindered by the challenges associated with long sampling periods and low-resolution image processing, prompting the development of various traditional methods to address these limitations. In recent times, advanced Deep Learning (DL) techniques have been applied to tackle the inverse problem of reconstructing MRI images from undersampled data. These DL models have demonstrated substantial improvements in terms of image reconstruction performance, cost-effectiveness, and reduced acquisition time, offering significant potential for further enhancements in this domain. This study introduces a novel DLGAN (Deep Learning Generative Adversarial Network) model comprising two sub-GAN modules tailored for specific datasets. Each module incorporates DLGAN (Generator Block, GB) and DLGAN (Discriminator Block, DB) blocks, strategically designed to regenerate MR images from K Space data. These blocks effectively leverage information from both the ground truth and KSpace characteristics, resulting in enhanced image reconstruction performance while also reducing complexity and improving overall efficiency. The DLGAN model effectively addresses common issues such as artefact removal and vanishing-gradient problems through the extraction of hierarchical features. To evaluate the model’s effectiveness, comprehensive experiments were conducted, utilizing metrics such as Peak Signal-to-Noise Ratio (PSNR) and Structural Similarity Index (SSIM). The experimental findings demonstrate that the proposed DLGAN model outperforms the most recent designs in MRI image reconstruction, showcasing its potential for significant advancements in clinical diagnosis and quantitative image analysis.

Feature Fusion for Multi-Coil Compressed MR Image Reconstruction.

Magnetic resonance imaging (MRI) occupies a pivotal position within contemporary diagnostic imaging modalities, offering non-invasive and radiation-free scanning. Despite its significance, MRI's principal limitation is the protracted data acquisition time, which hampers broader practical application. Promising deep learning (DL) methods for undersampled magnetic resonance (MR) image reconstruction outperform the traditional approaches in terms of speed and image quality. However, the intricate inter-coil correlations have been insufficiently addressed, leading to an underexploitation of the rich information inherent in multi-coil acquisitions. In this article, we proposed a method called "Multi-coil Feature Fusion Variation Network" (MFFVN), which introduces an encoder to extract the feature from multi-coil MR image directly and explicitly, followed by a feature fusion operation. Coil reshaping enables the 2D network to achieve satisfactory reconstruction results, while avoiding the introduction of a significant number of parameters and preserving inter-coil information. Compared with VN, MFFVN yields an improvement in the average PSNR and SSIM of the test set, registering enhancements of 0.2622dB and 0.0021dB respectively. This uplift can be attributed to the integration of feature extraction and fusion stages into the network's architecture, thereby effectively leveraging and combining the multi-coil information for enhanced image reconstruction quality. The proposed method outperforms the state-of-the-art methods on fastMRI dataset of multi-coil brains under a fourfold acceleration factor without incurring substantial computation overhead.

Wavelet-Improved Score-Based Generative Model for Medical Imaging.

The score-based generative model (SGM) has demonstrated remarkable performance in addressing challenging under-determined inverse problems in medical imaging. However, acquiring high-quality training datasets for these models remains a formidable task, especially in medical image reconstructions. Prevalent noise perturbations or artifacts in low-dose Computed Tomography (CT) or under-sampled Magnetic Resonance Imaging (MRI) hinder the accurate estimation of data distribution gradients, thereby compromising the overall performance of SGMs when trained with these data. To alleviate this issue, we propose a wavelet-improved denoising technique to cooperate with the SGMs, ensuring effective and stable training. Specifically, the proposed method integrates a wavelet sub-network and the standard SGM sub-network into a unified framework, effectively alleviating inaccurate distribution of the data distribution gradient and enhancing the overall stability. The mutual feedback mechanism between the wavelet sub-network and the SGM sub-network empowers the neural network to learn accurate scores even when handling noisy samples. This combination results in a framework that exhibits superior stability during the learning process, leading to the generation of more precise and reliable reconstructed images. During the reconstruction process, we further enhance the robustness and quality of the reconstructed images by incorporating regularization constraint. Our experiments, which encompass various scenarios of low-dose and sparse-view CT, as well as MRI with varying under-sampling rates and masks, demonstrate the effectiveness of the proposed method by significantly enhanced the quality of the reconstructed images. Especially, our method with noisy training samples achieves comparable results to those obtained using clean data. Our code at https://zenodo.org/record/8266123.

A cross-domain complex convolution neural network for undersampled magnetic resonance image reconstruction

To introduce a new cross-domain complex convolution neural network for accurate MR image reconstruction from undersampled k-space data. Most reconstruction methods utilize neural networks or cascade neural networks in either the image domain and/or the k-space domain. However, these methods encounter several challenges: 1) Applying neural networks directly in the k-space domain is suboptimal for feature extraction; 2) Classic image-domain networks have difficulty in fully extracting texture features; and 3) Existing cross-domain methods still face challenges in extracting and fusing features from both image and k-space domains simultaneously. In this work, we propose a novel deep-learning-based 2-D single-coil complex-valued MR reconstruction network termed TEID-Net. TEID-Net integrates three modules: 1) TE-Net, an image-domain-based sub-network designed to enhance contrast in input features by incorporating a Texture Enhancement Module; 2) ID-Net, an intermediate-domain sub-network tailored to operate in the image-Fourier space, with the specific goal of reducing aliasing artifacts realized by leveraging the superior incoherence property of the decoupled one-dimensional signals; and 3) TEID-Net, a cross-domain reconstruction network in which ID-Nets and TE-Nets are combined and cascaded to boost the quality of image reconstruction further. Extensive experiments have been conducted on the fastMRI and Calgary-Campinas datasets. Results demonstrate the effectiveness of the proposed TEID-Net in mitigating undersampling-induced artifacts and producing high-quality image reconstructions, outperforming several state-of-the-art methods while utilizing fewer network parameters. The cross-domain TEID-Net excels in restoring tissue structures and intricate texture details. The results illustrate that TEID-Net is particularly well-suited for regular Cartesian undersampling scenarios.

AI-based motion artifact severity estimation in undersampled MRI allowing for selection of appropriate reconstruction models.

Magnetic Resonance acquisition is a time consuming process, making it susceptible to patient motion during scanning. Even motion in the order of a millimeter can introduce severe blurring and ghosting artifacts, potentially necessitating re-acquisition. Magnetic Resonance Imaging (MRI) can be accelerated by acquiring only a fraction of k-space, combined with advanced reconstruction techniques leveraging coil sensitivity profiles and prior knowledge. Artificial intelligence (AI)-based reconstruction techniques have recently been popularized, but generally assume an ideal setting without intra-scanmotion. To retrospectively detect and quantify the severity of motion artifacts in undersampled MRI data. This may prove valuable as a safety mechanism for AI-based approaches, provide useful information to the reconstruction method, or prompt for re-acquisition while the patient is still in thescanner. We developed a deep learning approach that detects and quantifies motion artifacts in undersampled brain MRI. We demonstrate that synthetically motion-corrupted data can be leveraged to train the convolutional neural network (CNN)-based motion artifact estimator, generalizing well to real-world data. Additionally, we leverage the motion artifact estimator by using it as a selector for a motion-robust reconstruction model in case a considerable amount of motion was detected, and a high data consistency model otherwise. Training and validation were performed on 4387 and 1304 synthetically motion-corrupted images and their uncorrupted counterparts, respectively. Testing was performed on undersampled in vivo motion-corrupted data from 28 volunteers, where our model distinguished head motion from motion-free scans with 91% and 96% accuracy when trained on synthetic and on real data, respectively. It predicted a manually defined quality label ('Good', 'Medium' or 'Bad' quality) correctly in 76% and 85% of the time when trained on synthetic and real data, respectively. When used as a selector it selected the appropriate reconstruction network 93% of the time, achieving near optimal SSIMvalues. The proposed method quantified motion artifact severity in undersampled MRI data with high accuracy, enabling real-time motion artifact detection that can help improve the safety and quality of AI-basedreconstructions.

Dual states based reinforcement learning for fast MR scan and image reconstruction

Incomplete phase encoding with few phases is an effective under-sampling manner of fast Magnetic Resonance (MR) scan. The key is how to choose important slice-specific phases. Reinforcement Learning (RL) is powerful for sequential decision-making and therefore is feasible for slice-specific phase selection. Existing RL-based methods employ time-consuming reconstruction-oriented Deep Neural Networks (DNN) to generate/transit states from which phase selection and reward computation are performed. The advantage is that the selected phases and the corresponding partial k-space data match the DNN for image reconstruction. The disadvantage lies in the impossibility of deciding/selecting a phase in as short as several milliseconds required in the timings of a typical pulse sequence. To simultaneously keep the matching advantage and avoid the inefficiency disadvantage, we propose a dual-state-based RL framework. A visible Parameter-Free (PF) state obtained by inverse Fast Fourier transform and a hidden DNN state obtained by applying a time-consuming reconstruction-oriented DNN on the visible state are called dual states. Visible states are used as input of phase decision networks and hidden states are used for computing reward to evaluate the decision networks. Because the time-consuming hidden states are merely involved in training process and only efficient visible states are computed in inference process, the proposed method is very efficient. Moreover, we demonstrate that incorporating the phase-indicator vector (containing sequentially selected phases) as an additional input to the transformer used for reconstructing from undersampled MR images can significantly improve image reconstruction accuracy. Experiments on fastMRI dataset demonstrate effectiveness and efficiency of the proposed method.

Compressed SVD-based L + S model to reconstruct undersampled dynamic MRI data using parallel architecture.

Magnetic Resonance Imaging (MRI) is a highly demanded medical imaging system due to high resolution, large volumetric coverage, and ability to capture the dynamic and functional information of body organs e.g. cardiac MRI is employed to assess cardiac structure and evaluate blood flow dynamics through the cardiac valves. Long scan time is the main drawback of MRI, which makes it difficult for the patients to remain still during the scanning process. By collecting fewer measurements, MRI scan time can be shortened, but this undersampling causes aliasing artifacts in the reconstructed images. Advanced image reconstruction algorithms have been used in literature to overcome these undersampling artifacts. These algorithms are computationally expensive and require a long time for reconstruction which makes them infeasible for real-time clinical applications e.g. cardiac MRI. However, exploiting the inherent parallelism in these algorithms can help to reduce their computation time. Low-rank plus sparse (L+S) matrix decomposition model is a technique used in literature to reconstruct the highly undersampled dynamic MRI (dMRI) data at the expense of long reconstruction time. In this paper, Compressed Singular Value Decomposition (cSVD) model is used in L+S decomposition model (instead of conventional SVD) to reduce the reconstruction time. The results provide improved quality of the reconstructed images. Furthermore, it has been observed that cSVD and other parts of the L+S model possess highly parallel operations; therefore, a customized GPU based parallel architecture of the modified L+S model has been presented to further reduce the reconstruction time. Four cardiac MRI datasets (three different cardiac perfusion acquired from different patients and one cardiac cine data), each with different acceleration factors of 2, 6 and 8 are used for experiments in this paper. Experimental results demonstrate that using the proposed parallel architecture for the reconstruction of cardiac perfusion data provides a speed-up factor up to 19.15× (with memory latency) and 70.55× (without memory latency) in comparison to the conventional CPU reconstruction with no compromise on image quality. The proposed method is well-suited for real-time clinical applications, offering a substantial reduction in reconstruction time.

DC-SiamNet: Deep contrastive Siamese network for self-supervised MRI reconstruction

Reconstruction methods based on deep learning have greatly shortened the data acquisition time of magnetic resonance imaging (MRI). However, these methods typically utilize massive fully sampled data for supervised training, restricting their application in certain clinical scenarios and posing challenges to the reconstruction effect when high-quality MR images are unavailable. Recently, self-supervised methods have been developed that only undersampled MRI images participate in the network training. Nevertheless, due to the lack of complete referable MR image data, self-supervised reconstruction is prone to produce incorrect structure contents, such as unnatural texture details and over-smoothed tissue sites. To solve this problem, we propose a self-supervised Deep Contrastive Siamese Network (DC-SiamNet) for fast MR imaging. First, DC-SiamNet performs the reconstruction with a Siamese unrolled structure and obtains visual representations in different iterative phases. Particularly, an attention-weighted average pooling module is employed at the bottleneck layer of the U-shape regularization unit, which can effectively aggregate valuable local information of the underlying feature map in the generated representation vector. Then, a novel hybrid loss function is designed to drive the self-supervised reconstruction and contrastive learning simultaneously by forcing the output consistency across different branches in the frequency domain, the image domain, and the latent space. The proposed method is extensively evaluated with different sampling patterns on the IXI brain dataset and the MRINet knee dataset. Experimental results show that DC-SiamNet can achieve 0.93 in structural similarity and 33.984 dB in peak signal-to-noise ratio on the IXI brain dataset under 8x acceleration. It has better reconstruction accuracy than other methods, and the performance is close to the corresponding model trained with full supervision, especially when the sampling rate is low. In addition, generalization experiments verify that our method has a strong cross-domain reconstruction ability for different contrast brain images.

Perceptual contrast and residual self-attention generative adversarial network-based for highly under-sampled MRI reconstruction

ObjectiveThe study of deep learning-based fast magnetic resonance imaging (MRI) reconstruction methods has become popular in recent years. However, it is still challenging to obtain high-fidelity MRI images from undersampled data with large acceleration factors. The objective of this study was to improve the reconstruction quality of under-sampled MR images by exploring the correlation between pixels in the image and the perceptual similarities between the initial reconstructed images and the fully sampled ones. MethodsExisting reconstruction methods often suffer from aliasing artefacts and blurry texture information. We propose a novel perceptual residual self-attention generative adversarial model, SRSAGAN, to tackle this issue for fast and accurate MRI reconstruction. The proposed method involves two operation steps. In step 1, leveraging the average information and similarity weights of high-level features, we designed a novel feature enhancement module based on residual self-attention to restore fine texture details in the reconstructed image. In step 2, to improve the accuracy of network inference, we compare the perceptual similarities between the initial reconstructed images and the fully sampled ones. ResultThe proposed algorithm was evaluated using the fastMRI dataset. It demonstrates that SRSAGAN outperforms state-of-art methods and reconstructs complex image texture with only 10 % retained the k-space raw data (10-fold acceleration). The reconstruction time is only about 7.78 ms.

J-LOUCR: Joint learned optimized undersampling and constrained reconstruction for accelerated MRI by reference-driven deep image prior

Undersampled magnetic resonance (MR) image reconstruction performance is related to two fundamental problems: where to sample and how to reconstruct the image. Previously developed deep learning-based magnetic resonance imaging (MRI) methods, including undersampled mask optimization and reconstruction, require large-scale, high-quality, and patient-based datasets for training, which presents a challenge in practical clinical scenarios. To reduce the dependence on datasets and perform undersampling and reconstruction simultaneously, we propose a novel joint learned optimized undersampling and constrained reconstruction method for accelerated MRI by a reference-driven deep image prior (J-LOUCR). Inspired by the deep image prior (DIP), J-LOUCR involves no pretraining procedure, resulting in no dependence on large-scale training datasets. The implementation of J-LOUCR includes learned optimization of the undersampled mask and constrained reconstruction with the reference-driven DIP. In the first step, based on the traditional DIP, we introduce a reference image as the network input and propose a joint optimization problem of the undersampled mask and network parameters. Then, the joint optimization problem is deconstructed into subproblems and solved by using the alternative iteration strategy to obtain the optimal undersampled mask guided by the reference image. In the second step, for the optimal undersampled mask, we consider and recommend that the structural similarity between the reference and target MR images be used as prior information. Under the dual drivers of the reference image as the network input and prior constraint, J-LOUCR optimizes the network parameters and then completes reconstruction. Experiments on invivo MR scans demonstrate that J-LOUCR can achieve more accurate reconstruction with more details and features.

REUSED: A deep neural network method for rapid whole-brain high-resolution myelin water fraction mapping from extremely under-sampled MRI.

Changes in myelination are a cardinal feature of brain development and the pathophysiology of several central nervous system diseases, including multiple sclerosis and dementias. Advanced magnetic resonance imaging (MRI) methods have been developed to probe myelin content through the measurement of myelin water fraction (MWF). However, the prolonged data acquisition and post-processing times of current MWF mapping methods pose substantial hurdles to their clinical implementation. Recently, fast steady-state MRI sequences have been implemented to produce high-spatial resolution whole-brain MWF mapping within ∼20min. Despite the subsequent significant advances in the inversion algorithm to derive MWF maps from steady-state MRI, the high-dimensional nature of such inversion does not permit further reduction of the acquisition time by data under-sampling. In this work, we present an unprecedented reduction in the computation (∼30s) and the acquisition time (∼7min) required for whole-brain high-resolution MWF mapping through a new Neural Network (NN)-based approach, named NN-Relaxometry of Extremely Under-SamplEd Data (NN-REUSED). Our analyses demonstrate virtually similar accuracy and precision in derived MWF values using NN-REUSED compared to results derived from the fully sampled reference method. The reduction in the acquisition and computation times represents a breakthrough toward clinically practical MWF mapping.

Sinogram upsampling using Primal–Dual UNet for undersampled CT and radial MRI reconstruction

Computed tomography (CT) and magnetic resonance imaging (MRI) are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal–Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal–Dual UNet, which improves the Primal–Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932±0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919±0.016. Furthermore, the proposed model resulted in 0.903±0.019 and 0.957±0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867±0.025 and 0.949±0.025. Finally, this paper shows that the proposed network not only improves the overall image quality, but also improves the image quality for the regions-of-interest: liver, kidneys, and spleen; as well as generalises better than the baselines in presence the of a needle.

Machine learning based priors for Bayesian inversion in MR imaging

The Bayesian approach allows the incorporation of informative prior knowledge to effectively enable and improve the solution of inverse problems. Obtaining prior information in probabilistic terms is, however, a challenging task. Recently, machine learning has been applied for the training of generative models to facilitate the translation of historically or otherwise available data to a prior distribution. In this work, we apply this methodology to undersampled magnetic resonance imaging. In particular, we employ an autoencoder as part of a generative model to statistically regularise and solve the high-dimensional inverse problem using Bayesian inversion. Comparison with a classical Gaussian Markov random field prior is performed and numerical examples highlight the possible advantages of data-driven priors.

A predictive signal model for dynamic cardiac magnetic resonance imaging

Robust dynamic cardiac magnetic resonance imaging (MRI) has been a long-standing endeavor—as real-time imaging can provide information on the temporal signatures of disease we currently cannot assess—with the past decade seeing remarkable advances in acceleration using compressed sensing (CS) and artificial intelligence (AI). However, substantial limitations to real-time imaging remain and reconstruction quality is not always guaranteed. To improve reconstruction fidelity in dynamic cardiac MRI, we propose a novel predictive signal model that uses a priori statistics to adaptively predict temporal cardiac dynamics. By using a small training set obtained from the same patient, the new signal model can achieve robust dynamic cardiac MRI in the presence of irregular cardiac rhythm. Evaluation on simulated irregular cardiac dynamics and prospectively undersampled clinical cardiac MRI data demonstrate improved reconstruction quality for two reconstruction frameworks: Kalman filter and CS. The predictive model also works with different undersampling patterns (cartesian, radial, spiral) and can serve as a versatile foundation for robust dynamic cardiac MRI.

Optimizing data acquisition in undersampled magnetic resonance imaging (MRI) using two alternative forced choice (2-AFC) and search tasks.

Undersampling in the frequency domain (k-space) in MRI accelerates the data acquisition. Typically, a fraction of the low frequencies is fully collected and the rest are equally undersampled. We used a fixed 1D undersampling factor of 5x where 20% of the k-space lines are collected but varied the fraction of the low k-space frequencies that are fully sampled. We used a range of fully acquired low k-space frequencies from 0% where the primary artifact is aliasing to 20% where the primary artifact is blurring in the undersampling direction. Small lesions were placed in the coil k-space data for fluid-attenuated inversion recovery (FLAIR) brain images from the fastMRI database. The images were reconstructed using a multi-coil SENSE reconstruction with no regularization. We conducted a human observer two-alternative forced choice (2-AFC) study with a signal known exactly and a search task with variable backgrounds for each of the acquisitions. We found that for the 2-AFC task, the average human observer did better with more of the low frequencies being fully sampled. For the search task, we found that after an initial improvement from having none of the low frequencies fully sampled to just 2.5%, the performance remained fairly constant. We found that the performance in the two tasks had a different relationship to the acquired data. We also found that the search task was more consistent with common practice in MRI where a range of frequencies between 5% and 10% of the low frequencies are fully sampled.