Complex Fully Convolutional Neural Networks for MR Image Reconstruction

Undersampling the k-space data is widely adopted for acceleration of Magnetic Resonance Imaging (MRI). Current deep learning based approaches for supervised learning of MRI image reconstruction employ real-valued operations and representations by treating complex valued k-space/spatial-space as real values. In this paper, we propose complex dense fully convolutional neural network ($\mathbb{C}$DFNet) for learning to de-alias the reconstruction artifacts within undersampled MRI images. We fashioned a densely-connected fully convolutional block tailored for complex-valued inputs by introducing dedicated layers such as complex convolution, batch normalization, non-linearities etc. $\mathbb{C}$DFNet leverages the inherently complex-valued nature of input k-space and learns richer representations. We demonstrate improved perceptual quality and recovery of anatomical structures through $\mathbb{C}$DFNet in contrast to its real-valued counterparts.Comment: 9 pages, accepted in MICCAI-MLMIR 2018 Worsho

Analysis of Deep Complex-Valued Convolutional Neural Networks for MRI Reconstruction

Many real-world signal sources are complex-valued, having real and imaginary components. However, the vast majority of existing deep learning platforms and network architectures do not support the use of complex-valued data. MRI data is inherently complex-valued, so existing approaches discard the richer algebraic structure of the complex data. In this work, we investigate end-to-end complex-valued convolutional neural networks - specifically, for image reconstruction in lieu of two-channel real-valued networks. We apply this to magnetic resonance imaging reconstruction for the purpose of accelerating scan times and determine the performance of various promising complex-valued activation functions. We find that complex-valued CNNs with complex-valued convolutions provide superior reconstructions compared to real-valued convolutions with the same number of trainable parameters, over a variety of network architectures and 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

DIMENSION: Dynamic MR Imaging with Both K-space and Spatial Prior Knowledge Obtained via Multi-Supervised Network Training

Dynamic MR image reconstruction from incomplete k-space data has generated great research interest due to its capability in reducing scan time. Nevertheless, the reconstruction problem is still challenging due to its ill-posed nature. Most existing methods either suffer from long iterative reconstruction time or explore limited prior knowledge. This paper proposes a dynamic MR imaging method with both k-space and spatial prior knowledge integrated via multi-supervised network training, dubbed as DIMENSION. Specifically, the DIMENSION architecture consists of a frequential prior network for updating the k-space with its network prediction and a spatial prior network for capturing image structures and details. Furthermore, a multisupervised network training technique is developed to constrain the frequency domain information and reconstruction results at different levels. The comparisons with classical k-t FOCUSS, k-t SLR, L+S and the state-of-the-art CNN-based method on in vivo datasets show our method can achieve improved reconstruction results in shorter time.Comment: 11 pages, 12 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

Fidelity Imposed Network Edit (FINE) for Solving Ill-Posed Image Reconstruction

Deep learning (DL) is increasingly used to solve ill-posed inverse problems in imaging, such as reconstruction from noisy or incomplete data, as DL offers advantages over explicit image feature extractions in defining the needed prior. However, DL typically does not incorporate the precise physics of data generation or data fidelity. Instead, DL networks are trained to output some average response to an input. Consequently, DL image reconstruction contains errors, and may perform poorly when the test data deviates significantly from the training data, such as having new pathological features. To address this lack of data fidelity problem in DL image reconstruction, a novel approach, which we call fidelity-imposed network edit (FINE), is proposed. In FINE, a pre-trained prior network's weights are modified according to the physical model, on a test case. Our experiments demonstrate that FINE can achieve superior performance in two important inverse problems in neuroimaging: quantitative susceptibility mapping (QSM) and under-sampled reconstruction in MRI

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

Accelerating MR Imaging via Deep Chambolle-Pock Network

Compressed sensing (CS) has been introduced to accelerate data acquisition in MR Imaging. However, CS-MRI methods suffer from detail loss with large acceleration and complicated parameter selection. To address the limitations of existing CS-MRI methods, a model-driven MR reconstruction is proposed that trains a deep network, named CP-net, which is derived from the Chambolle-Pock algorithm to reconstruct the in vivo MR images of human brains from highly undersampled complex k-space data acquired on different types of MR scanners. The proposed deep network can learn the proximal operator and parameters among the Chambolle-Pock algorithm. All of the experiments show that the proposed CP-net achieves more accurate MR reconstruction results, outperforming state-of-the-art methods across various quantitative metrics.Comment: 4 pages, 5 figures, 1 table, Accepted at 2019 IEEE 41st Engineering in Medicine and Biology Conference (EMBC 2019

Fast PET reconstruction using Multi-scale Fully Convolutional Neural Networks

Reconstruction of PET images is an ill-posed inverse problem and often requires iterative algorithms to achieve good image quality for reliable clinical use in practice, at huge computational costs. In this paper, we consider the PET reconstruction a dense prediction problem where the large scale contextual information is essential, and propose a novel architecture of multi-scale fully convolutional neural networks (msfCNN) for fast PET image reconstruction. The proposed msfCNN gains large receptive fields with both memory and computational efficiency, by using a downscaling-upscaling structure and dilated convolutions. Instead of pooling and deconvolution, we propose to use the periodic shuffling operation from sub-pixel convolution and its inverse to scale the size of feature maps without losing resolution. Residual connections were added to improve training. We trained the proposed msfCNN model with simulated data, and applied it to clinical PET data acquired on a Siemens mMR scanner. The results from real oncological and neurodegenerative cases show that the proposed msfCNN-based reconstruction outperforms the iterative approaches in terms of computational time while achieving comparable image quality for quantification. The proposed msfCNN model can be applied to other dense prediction tasks, and fast msfCNN-based PET reconstruction could facilitate the potential use of molecular imaging in interventional/surgical procedures, where cancer surgery can particularly benefit

Convolutional Recurrent Neural Networks for Dynamic MR Image Reconstruction

Accelerating the data acquisition of dynamic magnetic resonance imaging (MRI) leads to a challenging ill-posed inverse problem, which has received great interest from both the signal processing and machine learning community over the last decades. The key ingredient to the problem is how to exploit the temporal correlation of the MR sequence to resolve the aliasing artefact. Traditionally, such observation led to a formulation of a non-convex optimisation problem, which were solved using iterative algorithms. Recently, however, deep learning based-approaches have gained significant popularity due to its ability to solve general inversion problems. In this work, we propose a unique, novel convolutional recurrent neural network (CRNN) architecture which reconstructs high quality cardiac MR images from highly undersampled k-space data by jointly exploiting the dependencies of the temporal sequences as well as the iterative nature of the traditional optimisation algorithms. In particular, the proposed architecture embeds the structure of the traditional iterative algorithms, efficiently modelling the recurrence of the iterative reconstruction stages by using recurrent hidden connections over such iterations. In addition, spatiotemporal dependencies are simultaneously learnt by exploiting bidirectional recurrent hidden connections across time sequences. The proposed algorithm is able to learn both the temporal dependency and the iterative reconstruction process effectively with only a very small number of parameters, while outperforming current MR reconstruction methods in terms of computational complexity, reconstruction accuracy and speed.Comment: Published in IEEE Transactions on Medical Imagin