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In this work, we propose a novel image reconstruction framework that directly learns a neural implicit representation in k-space for ECG-triggered non-Cartesian Cardiac Magnetic Resonance Imaging (CMR). While existing methods bin acquired data from neighboring time points to reconstruct one phase of the cardiac motion, our framework allows for a continuous, binning-free, and subject-specific k-space representation.We assign a unique coordinate that consists of time, coil index, and frequency domain location to each sampled k-space point. We then learn the subject-specific mapping from these unique coordinates to k-space intensities using a multi-layer perceptron with frequency domain regularization. During inference, we obtain a complete k-space for Cartesian coordinates and an arbitrary temporal resolution. A simple inverse Fourier transform recovers the image, eliminating the need for density compensation and costly non-uniform Fourier transforms for non-Cartesian data. This novel imaging framework was tested on 42 radially sampled datasets from 6 subjects. The proposed method outperforms other techniques qualitatively and quantitatively using data from four and one heartbeat(s) and 30 cardiac phases. Our results for one heartbeat reconstruction of 50 cardiac phases show improved artifact removal and spatio-temporal resolution, leveraging the potential for real-time CMR.

Cine cardiac magnetic resonance (CMR) imaging is considered the gold standard for cardiac function evaluation. However, cine CMR acquisition is inherently slow and in recent decades considerable effort has been put into accelerating scan times without compromising image quality or the accuracy of derived results. In this paper, we present a fully-automated, quality-controlled integrated framework for reconstruction, segmentation and downstream analysis of undersampled cine CMR data. The framework enables active acquisition of radial k-space data, in which acquisition can be stopped as soon as acquired data are sufficient to produce high quality reconstructions and segmentations. This results in reduced scan times and automated analysis, enabling robust and accurate estimation of functional biomarkers. To demonstrate the feasibility of the proposed approach, we perform realistic simulations of radial k-space acquisitions on a dataset of subjects from the UK Biobank and present results on in-vivo cine CMR k-space data collected from healthy subjects. The results demonstrate that our method can produce quality-controlled images in a mean scan time reduced from 12 to 4 seconds per slice, and that image quality is sufficient to allow clinically relevant parameters to be automatically estimated to within 5% mean absolute difference.

Cine cardiac MRI is routinely acquired for the assessment of cardiac health, but the imaging process is slow and typically requires several breath-holds to acquire sufficient k-space profiles to ensure good image quality. Several undersampling-based reconstruction techniques have been proposed during the last decades to speed up cine cardiac MRI acquisition. However, the undersampling factor is commonly fixed to conservative values before acquisition to ensure diagnostic image quality, potentially leading to unnecessarily long scan times. In this paper, we propose an end-to-end quality-aware cine short-axis cardiac MRI framework that combines image acquisition and reconstruction with downstream tasks such as segmentation, volume curve analysis and estimation of cardiac functional parameters. The goal is to reduce scan time by acquiring only a fraction of k-space data to enable the reconstruction of images that can pass quality control checks and produce reliable estimates of cardiac functional parameters. The framework consists of a deep learning model for the reconstruction of 2D+t cardiac cine MRI images from undersampled data, an image quality-control step to detect good quality reconstructions, followed by a deep learning model for bi-ventricular segmentation, a quality-control step to detect good quality segmentations and automated calculation of cardiac functional parameters. To demonstrate the feasibility of the proposed approach, we perform simulations using a cohort of selected participants from the UK Biobank (n=270), 200 healthy subjects and 70 patients with cardiomyopathies. Our results show that we can produce quality-controlled images in a scan time reduced from 12 to 4 seconds per slice, enabling reliable estimates of cardiac functional parameters such as ejection fraction within 5% mean absolute error.

Physiological motion, such as cardiac and respiratory motion, during Magnetic Resonance (MR) image acquisition can cause image artifacts. Motion correction techniques have been proposed to compensate for these types of motion during thoracic scans, relying on accurate motion estimation from undersampled motion-resolved reconstruction. A particular interest and challenge lie in the derivation of reliable non-rigid motion fields from the undersampled motion-resolved data. Motion estimation is usually formulated in image space via diffusion, parametric-spline, or optical flow methods. However, image-based registration can be impaired by remaining aliasing artifacts due to the undersampled motion-resolved reconstruction. In this work, we describe a formalism to perform non-rigid registration directly in the sampled Fourier space, i.e. k-space. We propose a deep-learning based approach to perform fast and accurate non-rigid registration from the undersampled k-space data. The basic working principle originates from the Local All-Pass (LAP) technique, a recently introduced optical flow-based registration. The proposed LAPNet is compared against traditional and deep learning image-based registrations and tested on fully-sampled and highly-accelerated (with two undersampling strategies) 3D respiratory motion-resolved MR images in a cohort of 40 patients with suspected liver or lung metastases and 25 healthy subjects. The proposed LAPNet provided consistent and superior performance to image-based approaches throughout different sampling trajectories and acceleration factors.

Purpose: Magnetization transfer (MT) and inhomogeneous MT (ihMT) contrasts are used in MRI to provide information about macromolecular tissue content. In particular, MT is sensitive to macromolecules and ihMT appears to be specific to myelinated tissue. This study proposes a technique to characterize MT and ihMT properties from a single acquisition, producing both semiquantitative contrast ratios, and quantitative parameter maps. Theory and Methods: Building upon previous work that uses multiband radiofrequency (RF) pulses to efficiently generate ihMT contrast, we propose a cyclic-steady-state approach that cycles between multiband and single-band pulses to boost the achieved contrast. Resultant time-variable signals are reminiscent of a magnetic resonance fingerprinting (MRF) acquisition, except that the signal fluctuations are entirely mediated by magnetization transfer effects. A dictionary-based low-rank inversion method is used to reconstruct the resulting images and to produce both semiquantitative MT ratio (MTR) and ihMT ratio (ihMTR) maps, as well as quantitative parameter estimates corresponding to an ihMT tissue model. Results: Phantom and in vivo brain data acquired at 1.5T demonstrate the expected contrast trends, with ihMTR maps showing contrast more specific to white matter (WM), as has been reported by others. Quantitative estimation of semisolid fraction and dipolar T1 was also possible and yielded measurements consistent with literature values in the brain. Conclusions: By cycling between multiband and single-band pulses, an entirely magnetization transfer mediated 'fingerprinting' method was demonstrated. This proof-of-concept approach can be used to generate semiquantitative maps and quantitatively estimate some macromolecular specific tissue parameters., Comment: 34 Pages and 15 Figures (Including Supporting Information), Submitted to Magnetic Resonance in Medicine (MRM). Updated to include link to final published article

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.

Segmenting anatomical structures in medical images has been successfully addressed with deep learning methods for a range of applications. However, this success is heavily dependent on the quality of the image that is being segmented. A commonly neglected point in the medical image analysis community is the vast amount of clinical images that have severe image artefacts due to organ motion, movement of the patient and/or image acquisition related issues. In this paper, we discuss the implications of image motion artefacts on cardiac MR segmentation and compare a variety of approaches for jointly correcting for artefacts and segmenting the cardiac cavity. The method is based on our recently developed joint artefact detection and reconstruction method, which reconstructs high quality MR images from k-space using a joint loss function and essentially converts the artefact correction task to an under-sampled image reconstruction task by enforcing a data consistency term. In this paper, we propose to use a segmentation network coupled with this in an end-to-end framework. Our training optimises three different tasks: 1) image artefact detection, 2) artefact correction and 3) image segmentation. We train the reconstruction network to automatically correct for motion-related artefacts using synthetically corrupted cardiac MR k-space data and uncorrected reconstructed images. Using a test set of 500 2D+time cine MR acquisitions from the UK Biobank data set, we achieve demonstrably good image quality and high segmentation accuracy in the presence of synthetic motion artefacts. We showcase better performance compared to various image correction architectures., Comment: Accepted for publication in IEEE TMI

In fully sampled cardiac MR (CMR) acquisitions, motion can lead to corruption of k-space lines, which can result in artefacts in the reconstructed images. In this paper, we propose a method to automatically detect and correct motion-related artefacts in CMR acquisitions during reconstruction from k-space data. Our correction method is inspired by work on undersampled CMR reconstruction, and uses deep learning to optimize a data-consistency term for under-sampled k-space reconstruction. Our main methodological contribution is the addition of a detection network to classify motion-corrupted k-space lines to convert the problem of artefact correction to a problem of reconstruction using the data consistency term. We train our network to automatically correct for motion-related artefacts using synthetically corrupted cine CMR k-space data as well as uncorrupted CMR images. Using a test set of 50 2D+time cine CMR datasets from the UK Biobank, we achieve good image quality in the presence of synthetic motion artefacts. We quantitatively compare our method with a variety of techniques for recovering good image quality and showcase better performance compared to state of the art denoising techniques with a PSNR of 37.1. Moreover, we show that our method preserves the quality of uncorrupted images and therefore can be also utilized as a general image reconstruction algorithm., Comment: Accepted to MICCAI 2019. arXiv admin note: text overlap with arXiv:1808.05130