Probabilistic atlas priors have been commonly used to derive adaptive and robust brain MRI segmentation algorithms. Widely-used neuroimage analysis pipelines rely heavily on these techniques, which are often computationally expensive. In contrast, there has been a recent surge of approaches that leverage deep learning to implement segmentation tools that are computationally efficient at test time. However, most of these strategies rely on learning from manually annotated images. These supervised deep learning methods are therefore sensitive to the intensity profiles in the training dataset. To develop a deep learning-based segmentation model for a new image dataset (e.g., of different contrast), one usually needs to create a new labeled training dataset, which can be prohibitively expensive, or rely on suboptimal ad hoc adaptation or augmentation approaches. In this paper, we propose an alternative strategy that combines a conventional probabilistic atlas-based segmentation with deep learning, enabling one to train a segmentation model for new MRI scans without the need for any manually segmented images. Our experiments include thousands of brain MRI scans and demonstrate that the proposed method achieves good accuracy for a brain MRI segmentation task for different MRI contrasts, requiring only approximately 15 seconds at test time on a GPU. The code is freely available at http://voxelmorph.mit.edu.
Deep learning has shown its great promise in various biomedical image segmentation tasks. Existing models are typically based on U-Net and rely on an encoder-decoder architecture with stacked local operators to aggregate long-range information gradually. However, only using the local operators limits the efficiency and effectiveness. In this work, we propose the non-local U-Nets, which are equipped with flexible global aggregation blocks, for biomedical image segmentation. These blocks can be inserted into U-Net as size-preserving processes, as well as down-sampling and up-sampling layers. We perform thorough experiments on the 3D multimodality isointense infant brain MR image segmentation task to evaluate the non-local U-Nets. Results show that our proposed models achieve top performances with fewer parameters and faster computation.
The task of medical image segmentation commonly involves an image reconstruction step to convert acquired raw data to images before any analysis. However, noises, artifacts and loss of information due to the reconstruction process are almost inevitable, which compromises the final performance of segmentation. We present a novel learning framework that performs magnetic resonance brain image segmentation directly from k-space data. The end-to-end framework consists of a unique task-driven attention module that recurrently utilizes intermediate segmentation estimation to facilitate image-domain feature extraction from the raw data, thus closely bridging the reconstruction and the segmentation tasks. In addition, to address the challenge of manual labeling, we introduce a novel workflow to generate labeled training data for segmentation by exploiting imaging modality simulators and digital phantoms. Extensive experimental results show that the proposed method outperforms several state-of-the-art methods.
Brain image segmentation is used for visualizing and quantifying anatomical structures of the brain. We present an automated ap-proach using 2D deep residual dilated networks which captures rich context information of different tissues for the segmentation of eight brain structures. The proposed system was evaluated in the MICCAI Brain Segmentation Challenge and ranked 9th out of 22 teams. We further compared the method with traditional U-Net using leave-one-subject-out cross-validation setting on the public dataset. Experimental results shows that the proposed method outperforms traditional U-Net (i.e. 80.9% vs 78.3% in averaged Dice score, 4.35mm vs 11.59mm in averaged robust Hausdorff distance) and is computationally efficient.
Accurate segmentation of brain tissue in magnetic resonance images (MRI) is a diffcult task due to different types of brain abnormalities. Using information and features from multimodal MRI including T1, T1-weighted inversion recovery (T1-IR) and T2-FLAIR and differential geometric features including the Jacobian determinant(JD) and the curl vector(CV) derived from T1 modality can result in a more accurate analysis of brain images. In this paper, we use the differential geometric information including JD and CV as image characteristics to measure the differences between different MRI images, which represent local size changes and local rotations of the brain image, and we can use them as one CNN channel with other three modalities (T1-weighted, T1-IR and T2-FLAIR) to get more accurate results of brain segmentation. We test this method on two datasets including IBSR dataset and MRBrainS datasets based on the deep voxelwise residual network, namely VoxResNet, and obtain excellent improvement over single modality or three modalities and increases average DSC(Cerebrospinal Fluid (CSF), Gray Matter (GM) and White Matter (WM)) by about 1.5% on the well-known MRBrainS18 dataset and about 2.5% on the IBSR dataset. Moreover, we discuss that one modality combined with its JD or CV information can replace the segmentation effect of three modalities, which can provide medical conveniences for doctor to diagnose because only to extract T1-modality MRI image of patients. Finally, we also compare the segmentation performance of our method in two networks, VoxResNet and U-Net network. The results show VoxResNet has a better performance than U-Net network with our method in brain MRI segmentation. We believe the proposed method can advance the performance in brain segmentation and clinical diagnosis.
We address the problem of segmenting 3D multi-modal medical images in scenarios where very few labeled examples are available for training. Leveraging the recent success of adversarial learning for semi-supervised segmentation, we propose a novel method based on Generative Adversarial Networks (GANs) to train a segmentation model with both labeled and unlabeled images. The proposed method prevents over-fitting by learning to discriminate between true and fake patches obtained by a generator network. Our work extends current adversarial learning approaches, which focus on 2D single-modality images, to the more challenging context of 3D volumes of multiple modalities. The proposed method is evaluated on the problem of segmenting brain MRI from the iSEG-2017 and MRBrainS 2013 datasets. Significant performance improvement is reported, compared to state-of-art segmentation networks trained in a fully-supervised manner. In addition, our work presents a comprehensive analysis of different GAN architectures for semi-supervised segmentation, showing recent techniques like feature matching to yield a higher performance than conventional adversarial training approaches. Our code is publicly available at https://github.com/arnab39/FewShot_GAN-Unet3D
Convolutional Neural Networks (CNNs) can be shifted across 2D images or 3D videos to segment them. They have a fixed input size and typically perceive only small local contexts of the pixels to be classified as foreground or background. In contrast, Multi-Dimensional Recurrent NNs (MD-RNNs) can perceive the entire spatio-temporal context of each pixel in a few sweeps through all pixels, especially when the RNN is a Long Short-Term Memory (LSTM). Despite these theoretical advantages, however, unlike CNNs, previous MD-LSTM variants were hard to parallelize on GPUs. Here we re-arrange the traditional cuboid order of computations in MD-LSTM in pyramidal fashion. The resulting PyraMiD-LSTM is easy to parallelize, especially for 3D data such as stacks of brain slice images. PyraMiD-LSTM achieved best known pixel-wise brain image segmentation results on MRBrainS13 (and competitive results on EM-ISBI12).
Electron microscopic connectomics is an ambitious research direction with the goal of studying comprehensive brain connectivity maps by using high-throughput, nano-scale microscopy. One of the main challenges in connectomics research is developing scalable image analysis algorithms that require minimal user intervention. Recently, deep learning has drawn much attention in computer vision because of its exceptional performance in image classification tasks. For this reason, its application to connectomic analyses holds great promise, as well. In this paper, we introduce a novel deep neural network architecture, FusionNet, for the automatic segmentation of neuronal structures in connectomics data. FusionNet leverages the latest advances in machine learning, such as semantic segmentation and residual neural networks, with the novel introduction of summation-based skip connections to allow a much deeper network architecture for a more accurate segmentation. We demonstrate the performance of the proposed method by comparing it with state-of-the-art electron microscopy (EM) segmentation methods from the ISBI EM segmentation challenge. We also show the segmentation results on two different tasks including cell membrane and cell body segmentation and a statistical analysis of cell morphology.
Image segmentation is the process of partitioning the image into significant regions easier to analyze. Nowadays, segmentation has become a necessity in many practical medical imaging methods as locating tumors and diseases. Hidden Markov Random Field model is one of several techniques used in image segmentation. It provides an elegant way to model the segmentation process. This modeling leads to the minimization of an objective function. Conjugate Gradient algorithm (CG) is one of the best known optimization techniques. This paper proposes the use of the Conjugate Gradient algorithm (CG) for image segmentation, based on the Hidden Markov Random Field. Since derivatives are not available for this expression, finite differences are used in the CG algorithm to approximate the first derivative. The approach is evaluated using a number of publicly available images, where ground truth is known. The Dice Coefficient is used as an objective criterion to measure the quality of segmentation. The results show that the proposed CG approach compares favorably with other variants of Hidden Markov Random Field segmentation algorithms.
Semantic segmentation is an established while rapidly evolving field in medical imaging. In this paper we focus on the segmentation of brain Magnetic Resonance Images (MRI) into cerebral structures using convolutional neural networks (CNN). CNNs achieve good performance by finding effective high dimensional image features describing the patch content only. In this work, we propose different ways to introduce spatial constraints into the network to further reduce prediction inconsistencies. A patch based CNN architecture was trained, making use of multiple scales to gather contextual information. Spatial constraints were introduced within the CNN through a distance to landmarks feature or through the integration of a probability atlas. We demonstrate experimentally that using spatial information helps to reduce segmentation inconsistencies.
NeuroNet is a deep convolutional neural network mimicking multiple popular and state-of-the-art brain segmentation tools including FSL, SPM, and MALPEM. The network is trained on 5,000 T1-weighted brain MRI scans from the UK Biobank Imaging Study that have been automatically segmented into brain tissue and cortical and sub-cortical structures using the standard neuroimaging pipelines. Training a single model from these complementary and partially overlapping label maps yields a new powerful "all-in-one", multi-output segmentation tool. The processing time for a single subject is reduced by an order of magnitude compared to running each individual software package. We demonstrate very good reproducibility of the original outputs while increasing robustness to variations in the input data. We believe NeuroNet could be an important tool in large-scale population imaging studies and serve as a new standard in neuroscience by reducing the risk of introducing bias when choosing a specific software package.