Compressed Sensing MRI via a Multi-scale Dilated Residual Convolution Network

Magnetic resonance imaging (MRI) reconstruction is an active inverse problem which can be addressed by conventional compressed sensing (CS) MRI algorithms that exploit the sparse nature of MRI in an iterative optimization-based manner. However, two main drawbacks of iterative optimization-based CSMRI methods are time-consuming and are limited in model capacity. Meanwhile, one main challenge for recent deep learning-based CSMRI is the trade-off between model performance and network size. To address the above issues, we develop a new multi-scale dilated network for MRI reconstruction with high speed and outstanding performance. Comparing to convolutional kernels with same receptive fields, dilated convolutions reduce network parameters with smaller kernels and expand receptive fields of kernels to obtain almost same information. To maintain the abundance of features, we present global and local residual learnings to extract more image edges and details. Then we utilize concatenation layers to fuse multi-scale features and residual learnings for better reconstruction. Compared with several non-deep and deep learning CSMRI algorithms, the proposed method yields better reconstruction accuracy and noticeable visual improvements. In addition, we perform the noisy setting to verify the model stability, and then extend the proposed model on a MRI super-resolution task.Comment: 27 pages and 13 figure

Deep Learning Methods for Parallel Magnetic Resonance Image Reconstruction

Following the success of deep learning in a wide range of applications, neural network-based machine learning techniques have received interest as a means of accelerating magnetic resonance imaging (MRI). A number of ideas inspired by deep learning techniques from computer vision and image processing have been successfully applied to non-linear image reconstruction in the spirit of compressed sensing for both low dose computed tomography and accelerated MRI. The additional integration of multi-coil information to recover missing k-space lines in the MRI reconstruction process, is still studied less frequently, even though it is the de-facto standard for currently used accelerated MR acquisitions. This manuscript provides an overview of the recent machine learning approaches that have been proposed specifically for improving parallel imaging. A general background introduction to parallel MRI is given that is structured around the classical view of image space and k-space based methods. Both linear and non-linear methods are covered, followed by a discussion of recent efforts to further improve parallel imaging using machine learning, and specifically using artificial neural networks. Image-domain based techniques that introduce improved regularizers are covered as well as k-space based methods, where the focus is on better interpolation strategies using neural networks. Issues and open problems are discussed as well as recent efforts for producing open datasets and benchmarks for the community.Comment: 14 pages, 7 figure

Method for motion artifact reduction using a convolutional neural network for dynamic contrast enhanced MRI of the liver

Purpose: To improve the quality of images obtained via dynamic contrast-enhanced MRI (DCE-MRI) that include motion artifacts and blurring using a deep learning approach. Methods: A multi-channel convolutional neural network (MARC) based method is proposed for reducing the motion artifacts and blurring caused by respiratory motion in images obtained via DCE-MRI of the liver. The training datasets for the neural network included images with and without respiration-induced motion artifacts or blurring, and the distortions were generated by simulating the phase error in k-space. Patient studies were conducted using a multi-phase T1-weighted spoiled gradient echo sequence for the liver containing breath-hold failures during data acquisition. The trained network was applied to the acquired images to analyze the filtering performance, and the intensities and contrast ratios before and after denoising were compared via Bland-Altman plots. Results: The proposed network was found to significantly reduce the magnitude of the artifacts and blurring induced by respiratory motion, and the contrast ratios of the images after processing via the network were consistent with those of the unprocessed images. Conclusion: A deep learning based method for removing motion artifacts in images obtained via DCE-MRI in the liver was demonstrated and validated.Comment: 11 pages, 6 figure

CRDN: Cascaded Residual Dense Networks for Dynamic MR Imaging with Edge-enhanced Loss Constraint

Dynamic magnetic resonance (MR) imaging has generated great research interest, as it can provide both spatial and temporal information for clinical diagnosis. However, slow imaging speed or long scanning time is still one of the challenges for dynamic MR imaging. Most existing methods reconstruct Dynamic MR images from incomplete k-space data under the guidance of compressed sensing (CS) or low rank theory, which suffer from long iterative reconstruction time. Recently, deep learning has shown great potential in accelerating dynamic MR. Our previous work proposed a dynamic MR imaging method with both k-space and spatial prior knowledge integrated via multi-supervised network training. Nevertheless, there was still a certain degree of smooth in the reconstructed images at high acceleration factors. In this work, we propose cascaded residual dense networks for dynamic MR imaging with edge-enhance loss constraint, dubbed as CRDN. Specifically, the cascaded residual dense networks fully exploit the hierarchical features from all the convolutional layers with both local and global feature fusion. We further utilize the total variation (TV) loss function, which has the edge enhancement properties, for training the networks

A Deep Information Sharing Network for Multi-contrast Compressed Sensing MRI Reconstruction

In multi-contrast magnetic resonance imaging (MRI), compressed sensing theory can accelerate imaging by sampling fewer measurements within each contrast. The conventional optimization-based models suffer several limitations: strict assumption of shared sparse support, time-consuming optimization and "shallow" models with difficulties in encoding the rich patterns hiding in massive MRI data. In this paper, we propose the first deep learning model for multi-contrast MRI reconstruction. We achieve information sharing through feature sharing units, which significantly reduces the number of parameters. The feature sharing unit is combined with a data fidelity unit to comprise an inference block. These inference blocks are cascaded with dense connections, which allows for information transmission across different depths of the network efficiently. Our extensive experiments on various multi-contrast MRI datasets show that proposed model outperforms both state-of-the-art single-contrast and multi-contrast MRI methods in accuracy and efficiency. We show the improved reconstruction quality can bring great benefits for the later medical image analysis stage. Furthermore, the robustness of the proposed model to the non-registration environment shows its potential in real MRI applications.Comment: 13 pages, 16 figures, 3 table

Self-Supervised Deep Active Accelerated MRI

We propose to simultaneously learn to sample and reconstruct magnetic resonance images (MRI) to maximize the reconstruction quality given a limited sample budget, in a self-supervised setup. Unlike existing deep methods that focus only on reconstructing given data, thus being passive, we go beyond the current state of the art by considering both the data acquisition and the reconstruction process within a single deep-learning framework. As our network learns to acquire data, the network is active in nature. In order to do so, we simultaneously train two neural networks, one dedicated to reconstruction and the other to progressive sampling, each with an automatically generated supervision signal that links them together. The two supervision signals are created through Monte Carlo tree search (MCTS). MCTS returns a better sampling pattern than what the current sampling network can give and, thus, a better final reconstruction. The sampling network is trained to mimic the MCTS results using the previous sampling network, thus being enhanced. The reconstruction network is trained to give the highest reconstruction quality, given the MCTS sampling pattern. Through this framework, we are able to train the two networks without providing any direct supervision on sampling

A Transfer-Learning Approach for Accelerated MRI using Deep Neural Networks

Purpose: Neural networks have received recent interest for reconstruction of undersampled MR acquisitions. Ideally network performance should be optimized by drawing the training and testing data from the same domain. In practice, however, large datasets comprising hundreds of subjects scanned under a common protocol are rare. The goal of this study is to introduce a transfer-learning approach to address the problem of data scarcity in training deep networks for accelerated MRI. Methods: Neural networks were trained on thousands of samples from public datasets of either natural images or brain MR images. The networks were then fine-tuned using only few tens of brain MR images in a distinct testing domain. Domain-transferred networks were compared to networks trained directly in the testing domain. Network performance was evaluated for varying acceleration factors (2-10), number of training samples (0.5-4k) and number of fine-tuning samples (0-100). Results: The proposed approach achieves successful domain transfer between MR images acquired with different contrasts (T1- and T2-weighted images), and between natural and MR images (ImageNet and T1- or T2-weighted images). Networks obtained via transfer-learning using only tens of images in the testing domain achieve nearly identical performance to networks trained directly in the testing domain using thousands of images. Conclusion: The proposed approach might facilitate the use of neural networks for MRI reconstruction without the need for collection of extensive imaging datasets

Deep Learning with Domain Adaptation for Accelerated Projection-Reconstruction MR

Purpose: The radial k-space trajectory is a well-established sampling trajectory used in conjunction with magnetic resonance imaging. However, the radial k-space trajectory requires a large number of radial lines for high-resolution reconstruction. Increasing the number of radial lines causes longer acquisition time, making it more difficult for routine clinical use. On the other hand, if we reduce the number of radial lines, streaking artifact patterns are unavoidable. To solve this problem, we propose a novel deep learning approach with domain adaptation to restore high-resolution MR images from under-sampled k-space data. Methods: The proposed deep network removes the streaking artifacts from the artifact corrupted images. To address the situation given the limited available data, we propose a domain adaptation scheme that employs a pre-trained network using a large number of x-ray computed tomography (CT) or synthesized radial MR datasets, which is then fine-tuned with only a few radial MR datasets. Results: The proposed method outperforms existing compressed sensing algorithms, such as the total variation and PR-FOCUSS methods. In addition, the calculation time is several orders of magnitude faster than the total variation and PR-FOCUSS methods.Moreover, we found that pre-training using CT or MR data from similar organ data is more important than pre-training using data from the same modality for different organ. Conclusion: We demonstrate the possibility of a domain-adaptation when only a limited amount of MR data is available. The proposed method surpasses the existing compressed sensing algorithms in terms of the image quality and computation time.Comment: This paper has been accepted and will soon appear in Magnetic Resonance in Medicin

Reducing Uncertainty in Undersampled MRI Reconstruction with Active Acquisition

The goal of MRI reconstruction is to restore a high fidelity image from partially observed measurements. This partial view naturally induces reconstruction uncertainty that can only be reduced by acquiring additional measurements. In this paper, we present a novel method for MRI reconstruction that, at inference time, dynamically selects the measurements to take and iteratively refines the prediction in order to best reduce the reconstruction error and, thus, its uncertainty. We validate our method on a large scale knee MRI dataset, as well as on ImageNet. Results show that (1) our system successfully outperforms active acquisition baselines; (2) our uncertainty estimates correlate with error maps; and (3) our ResNet-based architecture surpasses standard pixel-to-pixel models in the task of MRI reconstruction. The proposed method not only shows high-quality reconstructions but also paves the road towards more applicable solutions for accelerating MRI

ADMM-Net: A Deep Learning Approach for Compressive Sensing MRI

Compressive sensing (CS) is an effective approach for fast Magnetic Resonance Imaging (MRI). It aims at reconstructing MR images from a small number of under-sampled data in k-space, and accelerating the data acquisition in MRI. To improve the current MRI system in reconstruction accuracy and speed, in this paper, we propose two novel deep architectures, dubbed ADMM-Nets in basic and generalized versions. ADMM-Nets are defined over data flow graphs, which are derived from the iterative procedures in Alternating Direction Method of Multipliers (ADMM) algorithm for optimizing a general CS-based MRI model. They take the sampled k-space data as inputs and output reconstructed MR images. Moreover, we extend our network to cope with complex-valued MR images. In the training phase, all parameters of the nets, e.g., transforms, shrinkage functions, etc., are discriminatively trained end-to-end. In the testing phase, they have computational overhead similar to ADMM algorithm but use optimized parameters learned from the data for CS-based reconstruction task. We investigate different configurations in network structures and conduct extensive experiments on MR image reconstruction under different sampling rates. Due to the combination of the advantages in model-based approach and deep learning approach, the ADMM-Nets achieve state-of-the-art reconstruction accuracies with fast computational speed