Knowing what you know in brain segmentation using Bayesian deep neural networks

In this paper, we describe a Bayesian deep neural network (DNN) for predicting FreeSurfer segmentations of structural MRI volumes, in minutes rather than hours. The network was trained and evaluated on a large dataset (n = 11,480), obtained by combining data from more than a hundred different sites, and also evaluated on another completely held-out dataset (n = 418). The network was trained using a novel spike-and-slab dropout-based variational inference approach. We show that, on these datasets, the proposed Bayesian DNN outperforms previously proposed methods, in terms of the similarity between the segmentation predictions and the FreeSurfer labels, and the usefulness of the estimate uncertainty of these predictions. In particular, we demonstrated that the prediction uncertainty of this network at each voxel is a good indicator of whether the network has made an error and that the uncertainty across the whole brain can predict the manual quality control ratings of a scan. The proposed Bayesian DNN method should be applicable to any new network architecture for addressing the segmentation problem.Comment: Submitted to Frontiers in Neuroinformatic

Sharing deep generative representation for perceived image reconstruction from human brain activity

Decoding human brain activities via functional magnetic resonance imaging (fMRI) has gained increasing attention in recent years. While encouraging results have been reported in brain states classification tasks, reconstructing the details of human visual experience still remains difficult. Two main challenges that hinder the development of effective models are the perplexing fMRI measurement noise and the high dimensionality of limited data instances. Existing methods generally suffer from one or both of these issues and yield dissatisfactory results. In this paper, we tackle this problem by casting the reconstruction of visual stimulus as the Bayesian inference of missing view in a multiview latent variable model. Sharing a common latent representation, our joint generative model of external stimulus and brain response is not only "deep" in extracting nonlinear features from visual images, but also powerful in capturing correlations among voxel activities of fMRI recordings. The nonlinearity and deep structure endow our model with strong representation ability, while the correlations of voxel activities are critical for suppressing noise and improving prediction. We devise an efficient variational Bayesian method to infer the latent variables and the model parameters. To further improve the reconstruction accuracy, the latent representations of testing instances are enforced to be close to that of their neighbours from the training set via posterior regularization. Experiments on three fMRI recording datasets demonstrate that our approach can more accurately reconstruct visual stimuli

Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images

We propose a novel attention gate (AG) model for medical image analysis that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules when using convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed AG models are evaluated on a variety of tasks, including medical image classification and segmentation. For classification, we demonstrate the use case of AGs in scan plane detection for fetal ultrasound screening. We show that the proposed attention mechanism can provide efficient object localisation while improving the overall prediction performance by reducing false positives. For segmentation, the proposed architecture is evaluated on two large 3D CT abdominal datasets with manual annotations for multiple organs. Experimental results show that AG models consistently improve the prediction performance of the base architectures across different datasets and training sizes while preserving computational efficiency. Moreover, AGs guide the model activations to be focused around salient regions, which provides better insights into how model predictions are made. The source code for the proposed AG models is publicly available.Comment: Accepted for Medical Image Analysis (Special Issue on Medical Imaging with Deep Learning). arXiv admin note: substantial text overlap with arXiv:1804.03999, arXiv:1804.0533

Abstracts of the 2014 Brains, Minds, and Machines Summer School

A compilation of abstracts from the student projects of the 2014 Brains, Minds, and Machines Summer School, held at Woods Hole Marine Biological Lab, May 29 - June 12, 2014.This work was supported by the Center for Brains, Minds and Machines (CBMM), funded by NSF STC award CCF-1231216

PSACNN: Pulse Sequence Adaptive Fast Whole Brain Segmentation

With the advent of convolutional neural networks~(CNN), supervised learning methods are increasingly being used for whole brain segmentation. However, a large, manually annotated training dataset of labeled brain images required to train such supervised methods is frequently difficult to obtain or create. In addition, existing training datasets are generally acquired with a homogeneous magnetic resonance imaging~(MRI) acquisition protocol. CNNs trained on such datasets are unable to generalize on test data with different acquisition protocols. Modern neuroimaging studies and clinical trials are necessarily multi-center initiatives with a wide variety of acquisition protocols. Despite stringent protocol harmonization practices, it is very difficult to standardize the gamut of MRI imaging parameters across scanners, field strengths, receive coils etc., that affect image contrast. In this paper we propose a CNN-based segmentation algorithm that, in addition to being highly accurate and fast, is also resilient to variation in the input acquisition. Our approach relies on building approximate forward models of pulse sequences that produce a typical test image. For a given pulse sequence, we use its forward model to generate plausible, synthetic training examples that appear as if they were acquired in a scanner with that pulse sequence. Sampling over a wide variety of pulse sequences results in a wide variety of augmented training examples that help build an image contrast invariant model. Our method trains a single CNN that can segment input MRI images with acquisition parameters as disparate as $T_1$-weighted and $T_2$-weighted contrasts with only $T_1$-weighted training data. The segmentations generated are highly accurate with state-of-the-art results~(overall Dice overlap$=0.94$), with a fast run time~($\approx$ 45 seconds), and consistent across a wide range of acquisition protocols.Comment: Typo in author name corrected. Greves -> Grev

Deep Learning of Static and Dynamic Brain Functional Networks for Early MCI Detection

While convolutional neural network (CNN) has been demonstrating powerful ability to learn hierarchical spatial features from medical images, it is still difficult to apply it directly to resting-state functional MRI (rs-fMRI) and the derived brain functional networks (BFNs). We propose a novel CNN framework to simultaneously learn embedded features from BFNs for brain disease diagnosis. Since BFNs can be built by considering both static and dynamic functional connectivity (FC), we first decompose rs-fMRI into multiple static BFNs with modified independent component analysis. Then, the voxel-wise variability in dynamic FC is used to quantify BFN dynamics. A set of paired 3D images representing static/dynamic BFNs can be fed into 3D CNNs, from which we can hierarchically and simultaneously learn static/dynamic BFN features. As a result, the dynamic BFN features can complement static BFN features and, at the meantime, different BFNs can help each other toward a joint and better classification. We validate our method with a publicly accessible, large cohort of rs-fMRI dataset in early-stage mild cognitive impairment (eMCI) diagnosis, which is one of the most challenging problems to the clinicians. By comparing with a conventional method, our method shows significant diagnostic performance improvement by almost 10%. This result demonstrates the effectiveness of deep learning in preclinical Alzheimer's disease diagnosis, based on the complex and high-dimensional voxel-wise spatiotemporal patterns of the resting-state brain functional connectomics. The framework provides a new but intuitive way to fully exploit deeply embedded diagnostic features from rs-fMRI for a better-individualized diagnosis of various neurological diseases