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Register a new userConvolutional Recurrent Neural Networks for Dynamic MR Image Reconstruction
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Added by
Chen Qin
Publication date
2017
fields
Informatics Engineering
and research's language is
English
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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.
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Inspired by recent advances in deep learning, we propose a framework for reconstructing dynamic sequences of 2D cardiac magnetic resonance (MR) images from undersampled data using a deep cascade of convolutional neural networks (CNNs) to accelerate the data acquisition process. In particular, we address the case where data is acquired using aggressive Cartesian undersampling. Firstly, we show that when each 2D image frame is reconstructed independently, the proposed method outperforms state-of-the-art 2D compressed sensing approaches such as dictionary learning-based MR image reconstruction, in terms of reconstruction error and reconstruction speed. Secondly, when reconstructing the frames of the sequences jointly, we demonstrate that CNNs can learn spatio-temporal correlations efficiently by combining convolution and data sharing approaches. We show that the proposed method consistently outperforms state-of-the-art methods and is capable of preserving anatomical structure more faithfully up to 11-fold undersampling. Moreover, reconstruction is very fast: each complete dynamic sequence can be reconstructed in less than 10s and, for the 2D case, each image frame can be reconstructed in 23ms, enabling real-time applications.
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.
The acquisition of Magnetic Resonance Imaging (MRI) is inherently slow. Inspired by recent advances in deep learning, we propose a framework for reconstructing MR images from undersampled data using a deep cascade of convolutional neural networks to accelerate the data acquisition process. We show that for Cartesian undersampling of 2D cardiac MR images, the proposed method outperforms the state-of-the-art compressed sensing approaches, such as dictionary learning-based MRI (DLMRI) reconstruction, in terms of reconstruction error, perceptual quality and reconstruction speed for both 3-fold and 6-fold undersampling. Compared to DLMRI, the error produced by the method proposed is approximately twice as small, allowing to preserve anatomical structures more faithfully. Using our method, each image can be reconstructed in 23 ms, which is fast enough to enable real-time applications.
We introduce a stop-code tolerant (SCT) approach to training recurrent convolutional neural networks for lossy image compression. Our methods introduce a multi-pass training method to combine the training goals of high-quality reconstructions in areas around stop-code masking as well as in highly-detailed areas. These methods lead to lower true bitrates for a given recursion count, both pre- and post-entropy coding, even using unstructured LZ77 code compression. The pre-LZ77 gains are achieved by trimming stop codes. The post-LZ77 gains are due to the highly unequal distributions of 0/1 codes from the SCT architectures. With these code compressions, the SCT architecture maintains or exceeds the image quality at all compression rates compared to JPEG and to RNN auto-encoders across the Kodak dataset. In addition, the SCT coding results in lower variance in image quality across the extent of the image, a characteristic that has been shown to be important in human ratings of image quality
Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com- bination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results comparing to the known DL-based 3D segmentation approaches.
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