Self-Supervised k-Space Regularization for Motion-Resolved Abdominal MRI Using Neural Implicit k-Space Representation

Neural implicit k-space representations have shown promising results for dynamic MRI at high temporal resolutions. Yet, their exclusive training in k-space limits the application of common image regularization methods to improve the final reconstruction. In this work, we introduce the concept of parallel imaging-inspired self-consistency (PISCO), which we incorporate as novel self-supervised k-space regularization enforcing a consistent neighborhood relationship. At no additional data cost, the proposed regularization significantly improves neural implicit k-space reconstructions on simulated data. Abdominal in-vivo reconstructions using PISCO result in enhanced spatio-temporal image quality compared to state-of-the-art methods. Code is available at https://github.com/vjspi/PISCO-NIK.

Unsupervised reconstruction of accelerated cardiac cine MRI using Neural Fields

Cardiac cine MRI is the gold standard for cardiac functional assessment, but the inherently slow acquisition process creates the necessity of reconstruction approaches for accelerated undersampled acquisitions. Several regularization approaches that exploit spatial-temporal redundancy have been proposed to reconstruct undersampled cardiac cine MRI. More recently, methods based on supervised deep learning have been also proposed to further accelerate acquisition and reconstruction. However, these techniques rely on usually large dataset for training, which are not always available. In this work, we propose an unsupervised approach based on implicit neural field representations for cardiac cine MRI (so called NF-cMRI). The proposed method was evaluated in in-vivo undersampled golden-angle radial multi-coil acquisitions for undersampling factors of 26x and 52x, achieving good image quality, and comparable spatial and improved temporal depiction than a state-of-the-art reconstruction technique.

A Deep Learning-based Integrated Framework for Quality-aware Undersampled Cine Cardiac MRI Reconstruction and Analysis

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.

Quality-aware Cine Cardiac MRI Reconstruction and Analysis from Undersampled k-space Data

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.

LAPNet: Non-rigid Registration derived in k-space for Magnetic Resonance Imaging

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.

Magnetization Transfer-Mediated MR Fingerprinting

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.

Complementary Time-Frequency Domain Networks for Dynamic Parallel MR Image Reconstruction

Purpose: To introduce a novel deep learning based approach for fast and high-quality dynamic multi-coil MR reconstruction by learning a complementary time-frequency domain network that exploits spatio-temporal correlations simultaneously from complementary domains. Theory and Methods: Dynamic parallel MR image reconstruction is formulated as a multi-variable minimisation problem, where the data is regularised in combined temporal Fourier and spatial (x-f) domain as well as in spatio-temporal image (x-t) domain. An iterative algorithm based on variable splitting technique is derived, which alternates among signal de-aliasing steps in x-f and x-t spaces, a closed-form point-wise data consistency step and a weighted coupling step. The iterative model is embedded into a deep recurrent neural network which learns to recover the image via exploiting spatio-temporal redundancies in complementary domains. Results: Experiments were performed on two datasets of highly undersampled multi-coil short-axis cardiac cine MRI scans. Results demonstrate that our proposed method outperforms the current state-of-the-art approaches both quantitatively and qualitatively. The proposed model can also generalise well to data acquired from a different scanner and data with pathologies that were not seen in the training set. Conclusion: The work shows the benefit of reconstructing dynamic parallel MRI in complementary time-frequency domains with deep neural networks. The method can effectively and robustly reconstruct high-quality images from highly undersampled dynamic multi-coil data ($16 \times$ and $24 \times$ yielding 15s and 10s scan times respectively) with fast reconstruction speed (2.8s). This could potentially facilitate achieving fast single-breath-hold clinical 2D cardiac cine imaging.

Channel Attention Networks for Robust MR Fingerprinting Matching

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.

A Survey on Deep Learning and Explainability for Automatic Image-based Medical Report Generation

Every year physicians face an increasing demand of image-based diagnosis from patients, a problem that can be addressed with recent artificial intelligence methods. In this context, we survey works in the area of automatic report generation from medical images, with emphasis on methods using deep neural networks, with respect to: (1) Datasets, (2) Architecture Design, (3) Explainability and (4) Evaluation Metrics. Our survey identifies interesting developments, but also remaining challenges. Among them, the current evaluation of generated reports is especially weak, since it mostly relies on traditional Natural Language Processing (NLP) metrics, which do not accurately capture medical correctness.

Deep Learning Based Detection and Correction of Cardiac MR Motion Artefacts During Reconstruction for High-Quality Segmentation

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. 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 quantitatively compare our method with a variety of techniques for jointly recovering image quality and performing image segmentation. We showcase better performance compared to state-of-the-art image correction techniques. Moreover, our method preserves the quality of uncorrupted images and therefore can be utilised as a global image reconstruction algorithm.