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Register a new userSelf-supervised Recurrent Neural Network for 4D Abdominal and In-utero MR Imaging
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Accurately estimating and correcting the motion artifacts are crucial for 3D image reconstruction of the abdominal and in-utero magnetic resonance imaging (MRI). The state-of-art methods are based on slice-to-volume registration (SVR) where multiple 2D image stacks are acquired in three orthogonal orientations. In this work, we present a novel reconstruction pipeline that only needs one orientation of 2D MRI scans and can reconstruct the full high-resolution image without masking or registration steps. The framework consists of two main stages: the respiratory motion estimation using a self-supervised recurrent neural network, which learns the respiratory signals that are naturally embedded in the asymmetry relationship of the neighborhood slices and cluster them according to a respiratory state. Then, we train a 3D deconvolutional network for super-resolution (SR) reconstruction of the sparsely selected 2D images using integrated reconstruction and total variation loss. We evaluate the classification accuracy on 5 simulated images and compare our results with the SVR method in adult abdominal and in-utero MRI scans. The results show that the proposed pipeline can accurately estimate the respiratory state and reconstruct 4D SR volumes with better or similar performance to the 3D SVR pipeline with less than 20% sparsely selected slices. The method has great potential to transform the 4D abdominal and in-utero MRI in clinical practice.
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In dynamic magnetic resonance (MR) imaging, low-rank plus sparse (L+S) decomposition, or robust principal component analysis (PCA), has achieved stunning performance. However, the selection of the parameters of L+S is empirical, and the acceleration rate is limited, which are common failings of iterative compressed sensing MR imaging (CS-MRI) reconstruction methods. Many deep learning approaches have been proposed to address these issues, but few of them use a low-rank prior. In this paper, a model-based low-rank plus sparse network, dubbed L+S-Net, is proposed for dynamic MR reconstruction. In particular, we use an alternating linearized minimization method to solve the optimization problem with low-rank and sparse regularization. Learned soft singular value thresholding is introduced to ensure the clear separation of the L component and S component. Then, the iterative steps are unrolled into a network in which the regularization parameters are learnable. We prove that the proposed L+S-Net achieves global convergence under two standard assumptions. Experiments on retrospective and prospective cardiac cine datasets show that the proposed model outperforms state-of-the-art CS and existing deep learning methods and has great potential for extremely high acceleration factors (up to 24x).
We consider using {bfem untrained neural networks} to solve the reconstruction problem of snapshot compressive imaging (SCI), which uses a two-dimensional (2D) detector to capture a high-dimensional (usually 3D) data-cube in a compressed manner. Various SCI systems have been built in recent years to capture data such as high-speed videos, hyperspectral images, and the state-of-the-art reconstruction is obtained by the deep neural networks. However, most of these networks are trained in an end-to-end manner by a large amount of corpus with sometimes simulated ground truth, measurement pairs. In this paper, inspired by the untrained neural networks such as deep image priors (DIP) and deep decoders, we develop a framework by integrating DIP into the plug-and-play regime, leading to a self-supervised network for spectral SCI reconstruction. Extensive synthetic and real data results show that the proposed algorithm without training is capable of achieving competitive results to the training based networks. Furthermore, by integrating the proposed method with a pre-trained deep denoising prior, we have achieved state-of-the-art results. {Our code is available at url{https://github.com/mengziyi64/CASSI-Self-Supervised}.}
Dual-view snapshot compressive imaging (SCI) aims to capture videos from two field-of-views (FoVs) using a 2D sensor (detector) in a single snapshot, achieving joint FoV and temporal compressive sensing, and thus enjoying the advantages of low-bandwidth, low-power, and low-cost. However, it is challenging for existing model-based decoding algorithms to reconstruct each individual scene, which usually require exhaustive parameter tuning with extremely long running time for large scale data. In this paper, we propose an optical flow-aided recurrent neural network for dual video SCI systems, which provides high-quality decoding in seconds. Firstly, we develop a diversity amplification method to enlarge the differences between scenes of two FoVs, and design a deep convolutional neural network with dual branches to separate different scenes from the single measurement. Secondly, we integrate the bidirectional optical flow extracted from adjacent frames with the recurrent neural network to jointly reconstruct each video in a sequential manner. Extensive results on both simulation and real data demonstrate the superior performance of our proposed model in a short inference time. The code and data are available at https://github.com/RuiyingLu/OFaNet-for-Dual-view-SCI.
Machine learning technologies using deep neural networks (DNNs), especially convolutional neural networks (CNNs), have made automated, accurate, and fast medical image analysis a reality for many applications, and some DNN-based medical image analysis systems have even been FDA-cleared. Despite the progress, challenges remain to build DNNs as reliable as human expert doctors. It is known that DNN classifiers may not be robust to noises: by adding a small amount of noise to an input image, a DNN classifier may make a wrong classification of the noisy image (i.e., in-distribution adversarial sample), whereas it makes the right classification of the clean image. Another issue is caused by out-of-distribution samples that are not similar to any sample in the training set. Given such a sample as input, the output of a DNN will become meaningless. In this study, we investigated the in-distribution (IND) and out-of-distribution (OOD) adversarial robustness of a representative CNN for lumbar disk shape reconstruction from spine MR images. To study the relationship between dataset size and robustness to IND adversarial attacks, we used a data augmentation method to create training sets with different levels of shape variations. We utilized the PGD-based algorithm for IND adversarial attacks and extended it for OOD adversarial attacks to generate OOD adversarial samples for model testing. The results show that IND adversarial training can improve the CNN robustness to IND adversarial attacks, and larger training datasets may lead to higher IND robustness. However, it is still a challenge to defend against OOD adversarial attacks.
Purpose: To develop an improved self-supervised learning strategy that efficiently uses the acquired data for training a physics-guided reconstruction network without a database of fully-sampled data. Methods: Currently self-supervised learning for physics-guided reconstruction networks splits acquired undersampled data into two disjoint sets, where one is used for data consistency (DC) in the unrolled network and the other to define the training loss. The proposed multi-mask self-supervised learning via data undersampling (SSDU) splits acquired measurements into multiple pairs of disjoint sets for each training sample, while using one of these sets for DC units and the other for defining loss, thereby more efficiently using the undersampled data. Multi-mask SSDU is applied on fully-sampled 3D knee and prospectively undersampled 3D brain MRI datasets, which are retrospectively subsampled to acceleration rate (R)=8, and compared to CG-SENSE and single-mask SSDU DL-MRI, as well as supervised DL-MRI when fully-sampled data is available. Results: Results on knee MRI show that the proposed multi-mask SSDU outperforms SSDU and performs closely with supervised DL-MRI, while significantly outperforming CG-SENSE. A clinical reader study further ranks the multi-mask SSDU higher than supervised DL-MRI in terms of SNR and aliasing artifacts. Results on brain MRI show that multi-mask SSDU achieves better reconstruction quality compared to SSDU and CG-SENSE. Reader study demonstrates that multi-mask SSDU at R=8 significantly improves reconstruction compared to single-mask SSDU at R=8, as well as CG-SENSE at R=2. Conclusion: The proposed multi-mask SSDU approach enables improved training of physics-guided neural networks without fully-sampled data, by enabling efficient use of the undersampled data with multiple masks.
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