Data Consistent CT Reconstruction from Insufficient Data with Learned Prior Images

Image reconstruction from insufficient data is common in computed tomography (CT), e.g., image reconstruction from truncated data, limited-angle data and sparse-view data. Deep learning has achieved impressive results in this field. However, the robustness of deep learning methods is still a concern for clinical applications due to the following two challenges: a) With limited access to sufficient training data, a learned deep learning model may not generalize well to unseen data; b) Deep learning models are sensitive to noise. Therefore, the quality of images processed by neural networks only may be inadequate. In this work, we investigate the robustness of deep learning in CT image reconstruction by showing false negative and false positive lesion cases. Since learning-based images with incorrect structures are likely not consistent with measured projection data, we propose a data consistent reconstruction (DCR) method to improve their image quality, which combines the advantages of compressed sensing and deep learning: First, a prior image is generated by deep learning. Afterwards, unmeasured projection data are inpainted by forward projection of the prior image. Finally, iterative reconstruction with reweighted total variation regularization is applied, integrating data consistency for measured data and learned prior information for missing data. The efficacy of the proposed method is demonstrated in cone-beam CT with truncated data, limited-angle data and sparse-view data, respectively. For example, for truncated data, DCR achieves a mean root-mean-square error of 24 HU and a mean structure similarity index of 0.999 inside the field-of-view for different patients in the noisy case, while the state-of-the-art U-Net method achieves 55 HU and 0.995 respectively for these two metrics.Comment: 10 pages, 9 figure

Computationally Efficient Deep Neural Network for Computed Tomography Image Reconstruction

Deep-neural-network-based image reconstruction has demonstrated promising performance in medical imaging for under-sampled and low-dose scenarios. However, it requires large amount of memory and extensive time for the training. It is especially challenging to train the reconstruction networks for three-dimensional computed tomography (CT) because of the high resolution of CT images. The purpose of this work is to reduce the memory and time consumption of the training of the reconstruction networks for CT to make it practical for current hardware, while maintaining the quality of the reconstructed images. We unrolled the proximal gradient descent algorithm for iterative image reconstruction to finite iterations and replaced the terms related to the penalty function with trainable convolutional neural networks (CNN). The network was trained greedily iteration by iteration in the image-domain on patches, which requires reasonable amount of memory and time on mainstream graphics processing unit (GPU). To overcome the local-minimum problem caused by greedy learning, we used deep UNet as the CNN and incorporated separable quadratic surrogate with ordered subsets for data fidelity, so that the solution could escape from easy local minimums and achieve better image quality. The proposed method achieved comparable image quality with state-of-the-art neural network for CT image reconstruction on 2D sparse-view and limited-angle problems on the low-dose CT challenge dataset.Comment: 33 pages, 14 figures, accepted by Medical Physic

Deriving Neural Network Architectures using Precision Learning: Parallel-to-fan beam Conversion

In this paper, we derive a neural network architecture based on an analytical formulation of the parallel-to-fan beam conversion problem following the concept of precision learning. The network allows to learn the unknown operators in this conversion in a data-driven manner avoiding interpolation and potential loss of resolution. Integration of known operators results in a small number of trainable parameters that can be estimated from synthetic data only. The concept is evaluated in the context of Hybrid MRI/X-ray imaging where transformation of the parallel-beam MRI projections to fan-beam X-ray projections is required. The proposed method is compared to a traditional rebinning method. The results demonstrate that the proposed method is superior to ray-by-ray interpolation and is able to deliver sharper images using the same amount of parallel-beam input projections which is crucial for interventional applications. We believe that this approach forms a basis for further work uniting deep learning, signal processing, physics, and traditional pattern recognition.Comment: Inproceedings GCPR 201

Generative Adversarial Network in Medical Imaging: A Review

Generative adversarial networks have gained a lot of attention in the computer vision community due to their capability of data generation without explicitly modelling the probability density function. The adversarial loss brought by the discriminator provides a clever way of incorporating unlabeled samples into training and imposing higher order consistency. This has proven to be useful in many cases, such as domain adaptation, data augmentation, and image-to-image translation. These properties have attracted researchers in the medical imaging community, and we have seen rapid adoption in many traditional and novel applications, such as image reconstruction, segmentation, detection, classification, and cross-modality synthesis. Based on our observations, this trend will continue and we therefore conducted a review of recent advances in medical imaging using the adversarial training scheme with the hope of benefiting researchers interested in this technique.Comment: 24 pages; v4; added missing references from before Jan 1st 2019; accepted to MedI

Deep artifact learning for compressed sensing and parallel MRI

Purpose: Compressed sensing MRI (CS-MRI) from single and parallel coils is one of the powerful ways to reduce the scan time of MR imaging with performance guarantee. However, the computational costs are usually expensive. This paper aims to propose a computationally fast and accurate deep learning algorithm for the reconstruction of MR images from highly down-sampled k-space data. Theory: Based on the topological analysis, we show that the data manifold of the aliasing artifact is easier to learn from a uniform subsampling pattern with additional low-frequency k-space data. Thus, we develop deep aliasing artifact learning networks for the magnitude and phase images to estimate and remove the aliasing artifacts from highly accelerated MR acquisition. Methods: The aliasing artifacts are directly estimated from the distorted magnitude and phase images reconstructed from subsampled k-space data so that we can get an aliasing-free images by subtracting the estimated aliasing artifact from corrupted inputs. Moreover, to deal with the globally distributed aliasing artifact, we develop a multi-scale deep neural network with a large receptive field. Results: The experimental results confirm that the proposed deep artifact learning network effectively estimates and removes the aliasing artifacts. Compared to existing CS methods from single and multi-coli data, the proposed network shows minimal errors by removing the coherent aliasing artifacts. Furthermore, the computational time is by order of magnitude faster. Conclusion: As the proposed deep artifact learning network immediately generates accurate reconstruction, it has great potential for clinical applications

Deep Convolutional Framelet Denosing for Low-Dose CT via Wavelet Residual Network

Model based iterative reconstruction (MBIR) algorithms for low-dose X-ray CT are computationally expensive. To address this problem, we recently proposed a deep convolutional neural network (CNN) for low-dose X-ray CT and won the second place in 2016 AAPM Low-Dose CT Grand Challenge. However, some of the texture were not fully recovered. To address this problem, here we propose a novel framelet-based denoising algorithm using wavelet residual network which synergistically combines the expressive power of deep learning and the performance guarantee from the framelet-based denoising algorithms. The new algorithms were inspired by the recent interpretation of the deep convolutional neural network (CNN) as a cascaded convolution framelet signal representation. Extensive experimental results confirm that the proposed networks have significantly improved performance and preserves the detail texture of the original images.Comment: This will appear in IEEE Transaction on Medical Imaging, a special issue of Machine Learning for Image Reconstructio

Deep Component Analysis via Alternating Direction Neural Networks

Despite a lack of theoretical understanding, deep neural networks have achieved unparalleled performance in a wide range of applications. On the other hand, shallow representation learning with component analysis is associated with rich intuition and theory, but smaller capacity often limits its usefulness. To bridge this gap, we introduce Deep Component Analysis (DeepCA), an expressive multilayer model formulation that enforces hierarchical structure through constraints on latent variables in each layer. For inference, we propose a differentiable optimization algorithm implemented using recurrent Alternating Direction Neural Networks (ADNNs) that enable parameter learning using standard backpropagation. By interpreting feed-forward networks as single-iteration approximations of inference in our model, we provide both a novel theoretical perspective for understanding them and a practical technique for constraining predictions with prior knowledge. Experimentally, we demonstrate performance improvements on a variety of tasks, including single-image depth prediction with sparse output constraints

AdaDepth: Unsupervised Content Congruent Adaptation for Depth Estimation

Supervised deep learning methods have shown promising results for the task of monocular depth estimation; but acquiring ground truth is costly, and prone to noise as well as inaccuracies. While synthetic datasets have been used to circumvent above problems, the resultant models do not generalize well to natural scenes due to the inherent domain shift. Recent adversarial approaches for domain adaption have performed well in mitigating the differences between the source and target domains. But these methods are mostly limited to a classification setup and do not scale well for fully-convolutional architectures. In this work, we propose AdaDepth - an unsupervised domain adaptation strategy for the pixel-wise regression task of monocular depth estimation. The proposed approach is devoid of above limitations through a) adversarial learning and b) explicit imposition of content consistency on the adapted target representation. Our unsupervised approach performs competitively with other established approaches on depth estimation tasks and achieves state-of-the-art results in a semi-supervised setting.Comment: CVPR 201

CT-To-MR Conditional Generative Adversarial Networks for Ischemic Stroke Lesion Segmentation

Infarcted brain tissue resulting from acute stroke readily shows up as hyperintense regions within diffusion-weighted magnetic resonance imaging (DWI). It has also been proposed that computed tomography perfusion (CTP) could alternatively be used to triage stroke patients, given improvements in speed and availability, as well as reduced cost. However, CTP has a lower signal to noise ratio compared to MR. In this work, we investigate whether a conditional mapping can be learned by a generative adversarial network to map CTP inputs to generated MR DWI that more clearly delineates hyperintense regions due to ischemic stroke. We detail the architectures of the generator and discriminator and describe the training process used to perform image-to-image translation from multi-modal CT perfusion maps to diffusion weighted MR outputs. We evaluate the results both qualitatively by visual comparison of generated MR to ground truth, as well as quantitatively by training fully convolutional neural networks that make use of generated MR data inputs to perform ischemic stroke lesion segmentation. Segmentation networks trained using generated CT-to-MR inputs result in at least some improvement on all metrics used for evaluation, compared with networks that only use CT perfusion input.Comment: Seventh IEEE International Conference on Healthcare Informatics (ICHI 2019

Unified Probabilistic Deep Continual Learning through Generative Replay and Open Set Recognition

We introduce a probabilistic approach to unify open set recognition with the prevention of catastrophic forgetting in deep continual learning, based on variational Bayesian inference. Our single model combines a joint probabilistic encoder with a generative model and a linear classifier that get shared across sequentially arriving tasks. In order to successfully distinguish unseen unknown data from trained known tasks, we propose to bound the class specific approximate posterior by fitting regions of high density on the basis of correctly classified data points. These bounds are further used to significantly alleviate catastrophic forgetting by avoiding samples from low density areas in generative replay. Our approach requires neither storing of old, nor upfront knowledge of future data, and is empirically validated on visual and audio tasks in class incremental, as well as cross-dataset scenarios across modalities