Compressed sensing (CS) utilizes the sparsity of magnetic resonance (MR) images to enable accurate reconstruction from undersampled k-space data. Recent CS methods have employed analytical sparsifying transforms such as wavelets, curvelets, and finite differences. In this paper, we propose a novel framework for adaptively learning the sparsifying transform (dictionary), and reconstructing the image simultaneously from highly undersampled k-space data. The sparsity in this framework is enforced on overlapping image patches emphasizing local structure. Moreover, the dictionary is adapted to the particular image instance thereby favoring better sparsities and consequently much higher undersampling rates. The proposed alternating reconstruction algorithm learns the sparsifying dictionary, and uses it to remove aliasing and noise in one step, and subsequently restores and fills-in the k-space data in the other step. Numerical experiments are conducted on MR images and on real MR data of several anatomies with a variety of sampling schemes. The results demonstrate dramatic improvements on the order of 4-18 dB in reconstruction error and doubling of the acceptable undersampling factor using the proposed adaptive dictionary as compared to previous CS methods. These improvements persist over a wide range of practical data signal-to-noise ratios, without any parameter tuning.

MR Image Reconstruction From Highly Undersampled k-Space Data by Dictionary Learning

Compressive Sensing (CS) is an effective approach for fast Magnetic Resonance Imaging (MRI). It aims at reconstructing MR image 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 computational speed, in this paper, we propose a novel deep architecture, dubbed ADMM-Net. ADMM-Net is defined over a data flow graph, which is derived from the iterative procedures in Alternating Direction Method of Multipliers (ADMM) algorithm for optimizing a CS-based MRI model. In the training phase, all parameters of the net, e.g., image transforms, shrinkage functions, etc., are discriminatively trained end-to-end using L-BFGS algorithm. In the testing phase, it has computational overhead similar to ADMM but uses optimized parameters learned from the training data for CS-based reconstruction task. Experiments on MRI image reconstruction under different sampling ratios in k-space demonstrate that it significantly improves the baseline ADMM algorithm and achieves high reconstruction accuracies with fast computational speed.

https://proceedings.neurips.cc/paper/2016/file/1679091c5a880faf6fb5e6087eb1b2dc-Paper.pdf

Deep ADMM-Net for compressive sensing MRI

Compressed sensing magnetic resonance imaging (CS-MRI) enables fast acquisition, which is highly desirable for numerous clinical applications. This can not only reduce the scanning cost and ease patient burden, but also potentially reduce motion artefacts and the effect of contrast washout, thus yielding better image quality. Different from parallel imaging-based fast MRI, which utilizes multiple coils to simultaneously receive MR signals, CS-MRI breaks the Nyquist–Shannon sampling barrier to reconstruct MRI images with much less required raw data. This paper provides a deep learning-based strategy for reconstruction of CS-MRI, and bridges a substantial gap between conventional non-learning methods working only on data from a single image, and prior knowledge from large training data sets. In particular, a novel conditional Generative Adversarial Networks-based model (DAGAN)-based model is proposed to reconstruct CS-MRI. In our DAGAN architecture, we have designed a refinement learning method to stabilize our U-Net based generator, which provides an end-to-end network to reduce aliasing artefacts. To better preserve texture and edges in the reconstruction, we have coupled the adversarial loss with an innovative content loss. In addition, we incorporate frequency-domain information to enforce similarity in both the image and frequency domains. We have performed comprehensive comparison studies with both conventional CS-MRI reconstruction methods and newly investigated deep learning approaches. Compared with these methods, our DAGAN method provides superior reconstruction with preserved perceptual image details. Furthermore, each image is reconstructed in about 5 ms, which is suitable for real-time processing.

/pdf/dagan-deep-de-aliasing-generative-adversarial-networks-for-3u7cltdv1j.pdf

DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruction

Computational and Mathematical Methods in Medicine

Multi-focus image fusion with a deep convolutional neural network

Magnetic resonance imaging has been benefited from compressed sensing in improving imaging speed. But the computation time of compressed sensing magnetic resonance imaging (CS-MRI) is relatively long due to its iterative reconstruction process. Recently, a patch-based nonlocal operator (PANO) has been applied in CS-MRI to significantly reduce the reconstruction error by making use of self-similarity in images. But the two major steps in PANO, learning similarities and performing 3D wavelet transform, require extensive computations. In this paper, a parallel architecture based on multicore processors is proposed to accelerate computations of PANO. Simulation results demonstrate that the acceleration factor approaches the number of CPU cores and overall PANO-based CS-MRI reconstruction can be accomplished in several seconds.

/pdf/parallel-computing-of-patch-based-nonlocal-operator-and-its-5ejiukej5i.pdf

Parallel computing of patch-based nonlocal operator and its application in compressed sensing MRI.

Background: Nuclear Magnetic Resonance (NMR) spectroscopy is an important
bio-engineering tool to determine the metabolic concentrations, molecule
structures and so on. The data acquisition time, however, is very long in
multi-dimensional NMR. To accelerate data acquisition, non-uniformly sampling
is an effective way but may encounter severe spectral distortions and
unfaithful quantitative measures when the acceleration factor is high.
Objective: To reconstruct high fidelity spectra from highly accelerated NMR and
achieve much better quantitative measures. Methods: A virtual peak (VIP)
approach is proposed to self-learn the prior spectral information, such as the
central frequency and peak lineshape, and then feed these information into the
reconstruction. The proposed method is further implemented with cloud computing
to facilitate online, open, and easy access. Results: Results on synthetic and
experimental data demonstrate that, compared with the state-of-the-art method,
the new approach provides much better reconstruction of low-intensity peaks and
significantly improves the quantitative measures, including the regression of
peak intensity, the distances between nuclear pairs, and concentrations of
metabolics in mixtures. Conclusion: Self-learning prior peak information can
improve the reconstruction and quantitative measures of spectra. Significance:
This approach enables highly accelerated NMR and may promote time-consuming
applications such as quantitative and time-resolved NMR experiments.

XCloud-VIP: Virtual Peak Enables Highly Accelerated NMR Spectroscopy and Faithful Quantitative Measures

—Recent deep learning is superior in providing high-quality images and ultra-fast reconstructions in accelerated magnetic resonance imaging (MRI). Faithful coil sensitivity estimation is vital for MRI reconstruction. However, most deep learning methods still rely on pre- estimated sensitivity maps and ignore their inaccuracy, resulting in the significant quality degradation of reconstructed images. In this work, we propose a Joint Deep Sensitivity estimation and Image reconstruction network, called JDSI. During the image artifacts removal, it gradually provides more faithful sensitivity maps, leading to greatly improved image reconstructions. To understand the behavior of the network, the mutual promotion of sensitivity estimation and image reconstruction is revealed through the visualization of network intermediate results. Results on in vivo datasets and radiologist reader study demonstrate that, the proposed JDSI achieves the state-of-the-art performance visually and quantitatively, especially when the accelerated factor is high. Additionally, JDSI owns nice robustness to abnormal subjects and different number of autocalibration signals.

A Faithful Deep Sensitivity Estimation for Accelerated Magnetic Resonance Imaging

Hypercomplex Low Rank Reconstruction for Nmr Spectroscopy with Cloud Computing ⋆

Multi-contrast magnetic resonance imaging (MRI) can provide richer diagnosis information. The data acquisition time, however, is increased than single-contrast imaging. To reduce this time, k-space undersampling is an effective way but a smart reconstruction algorithm is required to remove undersampling image artifacts. Traditional algorithms commonly explore the similarity of multi-contrast images through joint sparsity. However, these algorithms are time-consuming due to the iterative process and require adjusting hyperparameters manually. Recently, data-driven deep learning successfully overcome these limitations but the reconstruction error still needs to be further reduced. Here, we propose a Joint Group Sparsity-based Network (JGSN) for multi-contrast MRI reconstruction, which unrolls the iterative process of the joint sparsity algorithm. The designed network includes data consistency modules, learnable sparse transform modules, and joint group sparsity constraint modules. In particular, weights of different contrasts in the transform module are shared to reduce network parameters without sacrificing the quality of reconstruction. The experiments were performed on the retrospective undersampled brain and knee data. Experimental results on in vivo brain data and knee data show that our method consistently outperforms the state-of-the-art methods under different sampling patterns. 

Di Guo

Papers

Parallel computing of patch-based nonlocal operator and its application in compressed sensing MRI.

XCloud-VIP: Virtual Peak Enables Highly Accelerated NMR Spectroscopy and Faithful Quantitative Measures

A Faithful Deep Sensitivity Estimation for Accelerated Magnetic Resonance Imaging

Hypercomplex Low Rank Reconstruction for Nmr Spectroscopy with Cloud Computing ⋆

A Joint Group Sparsity-based deep learning for multi-contrast MRI reconstruction.