The need for fast acquisition and automatic analysis of MRI data is growing. Although compressed sensing magnetic resonance imaging (CS-MRI) has been studied to accelerate MRI by reducing k-space measurements, current techniques overlook downstream applications such as segmentation when doing image reconstruction. In this paper, we test the utility of CS-MRI when performing automatic segmentation and propose a unified deep neural network architecture called SegNetMRI for simultaneous CS-MRI reconstruction and segmentation. SegNetMRI uses an MRI reconstruction network with multiple cascaded blocks, each containing an encoder-decoder unit and a data fidelity unit, and a parallel MRI segmentation network having the same encoder-decoder structure. The two subnetworks are pre-trained and fine-tuned with shared reconstruction encoders. The outputs are merged into the final segmentation. Our experiments show that SegNetMRI can improve both the reconstruction and segmentation performance when using compressed measurements.
Recently, deep neural networks have been introduced to CS-MRI. Researchers have directly applied convolutional neural networks (CNN) to learn a direct mapping from the zero-filled MRI @math (obtained by zero-padding the unsampled positions in k-space) to the true MRI @cite_10 . A deep residual architecture was also proposed for this same mapping @cite_11 . Data fidelity terms have been incorporated into the deep neural network by @cite_0 to add more guidance. These deep learning based CS-MRI models have achieved higher reconstruction quality and faster reconstruction speed.
@cite_0 @cite_10 @cite_11
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Compressed sensing magnetic resonance imaging (CS-MRI) has provided theoretical foundations upon which the time-consuming MRI acquisition process can be accelerated. However, it primarily relies on iterative numerical solvers, which still hinders their adaptation in time-critical applications. In addition, recent advances in deep neural networks have shown their potential in computer vision and image processing, but their adaptation to MRI reconstruction is still in an early stage. In this paper, we propose a novel deep learning-based generative adversarial model, RefineGAN , for fast and accurate CS-MRI reconstruction. The proposed model is a variant of fully-residual convolutional autoencoder and generative adversarial networks (GANs), specifically designed for CS-MRI formulation; it employs deeper generator and discriminator networks with cyclic data consistency loss for faithful interpolation in the given under-sampled @math -space data. In addition, our solution leverages a chained network to further enhance the reconstruction quality. RefineGAN is fast and accurate—the reconstruction process is extremely rapid, as low as tens of milliseconds for reconstruction of a @math image, because it is one-way deployment on a feed-forward network, and the image quality is superior even for extremely low sampling rate (as low as 10 ) due to the data-driven nature of the method. We demonstrate that RefineGAN outperforms the state-of-the-art CS-MRI methods by a large margin in terms of both running time and image quality via evaluation using several open-source MRI databases. This paper proposes a deep learning approach for accelerating magnetic resonance imaging (MRI) using a large number of existing high quality MR images as the training datasets. An off-line convolutional neural network is designed and trained to identify the mapping relationship between the MR images obtained from zero-filled and fully-sampled k-space data. The network is not only capable of restoring fine structures and details but is also compatible with online constrained reconstruction methods. Experimental results on real MR data have shown encouraging performance of the proposed method for efficient and accurate imaging. Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models. Recently, very deep convolutional neural networks (CNNs) have shown outstanding performance in object recognition and have also been the first choice for dense classification problems such as semantic segmentation. However, repeated subsampling operations like pooling or convolution striding in deep CNNs lead to a significant decrease in the initial image resolution. Here, we present RefineNet, a generic multi-path refinement network that explicitly exploits all the information available along the down-sampling process to enable high-resolution prediction using long-range residual connections. In this way, the deeper layers that capture high-level semantic features can be directly refined using fine-grained features from earlier convolutions. The individual components of RefineNet employ residual connections following the identity mapping mindset, which allows for effective end-to-end training. Further, we introduce chained residual pooling, which captures rich background context in an efficient manner. We carry out comprehensive experiments and set new state-of-the-art results on seven public datasets. In particular, we achieve an intersection-over-union score of 83.4 on the challenging PASCAL VOC 2012 dataset, which is the best reported result to date.