A robust variational autoencoder using beta divergence.

The presence of outliers can severely degrade learned representations and performance of deep learning methods and hence disproportionately affect the training process, leading to incorrect conclusions about the data. For example, anomaly detection using deep generative models is typically only possible when similar anomalies (or outliers) are not present in the training data. Here we focus on variational autoencoders (VAEs).

Variability of Single Pulse Electrical Stimulation Responses Recorded with Intracranial Electroencephalography in Epileptic Patients.

Cohort studies of brain stimulations performed with stereo-electroencephalographic (SEEG) electrodes in epileptic patients allow to derive large scale functional connectivity. It is known, however, that brain responses to electrical or magnetic stimulation techniques are not always reproducible. Here, we study variability of responses to single pulse SEEG electrical stimulation.

A hybrid high-resolution anatomical MRI atlas with sub-parcellation of cortical gyri using resting fMRI.

We present a new high-quality, single-subject atlas with sub-millimeter voxel resolution, high SNR, and excellent gray-white tissue contrast to resolve fine anatomical details. The atlas is labeled into two parcellation schemes: 1) the anatomical BCI-DNI atlas, which is manually labeled based on known morphological and anatomical features, and 2) the hybrid USCBrain atlas, which incorporates functional information to guide the sub-parcellation of cerebral cortex. In both cases, we provide consistent volumetric and cortical surface-based parcellation and labeling.

Autoregression and Structured Low-Rank Modeling of Sinogram Neighborhoods.

Sinograms are commonly used to represent the raw data from tomographic imaging experiments. Although it is already well-known that sinograms posess some amount of redundancy, in this work, we present novel theory suggesting that sinograms will often possess substantial additional redundancies that have not been explicitly exploited by previous methods. Specifically, we derive that sinograms will often satisfy multiple simple data-dependent autoregression relationships.

Effective connectivity differs between focal cortical dysplasia types I and II.

Objective: To determine whether brain connectivity differs between focal cortical dysplasia (FCD) types I and II.

Methods: We compared cortico-cortical evoked potentials (CCEPs) as measures of effective brain connectivity in 25 FCD patients with drug-resistant focal epilepsy who underwent intracranial evaluation with stereo-electroencephalography (SEEG). We analyzed the amplitude and latency of CCEP responses following ictal-onset single-pulse electrical stimulation (iSPES).

PALMNUT: An Enhanced Proximal Alternating Linearized Minimization Algorithm with Application to Separate Regularization of Magnitude and Phase.

We introduce a new algorithm for complex image reconstruction with separate regularization of the image magnitude and phase. This optimization problem is interesting in many different image reconstruction contexts, although is nonconvex and can be difficult to solve. In this work, we first describe a novel implementation of the previous proximal alternating linearized minimization (PALM) algorithm to solve this optimization problem.

Combined diffusion-relaxometry microstructure imaging: Current status and future prospects.

Microstructure imaging seeks to noninvasively measure and map microscopic tissue features by pairing mathematical modeling with tailored MRI protocols. This article reviews an emerging paradigm that has the potential to provide a more detailed assessment of tissue microstructure-combined diffusion-relaxometry imaging. Combined diffusion-relaxometry acquisitions vary multiple MR contrast encodings-such as b-value, gradient direction, inversion time, and echo time-in a multidimensional acquisition space.

Local perturbation responses and checkerboard tests: Characterization tools for nonlinear MRI methods.

Purpose: Modern methods for MR image reconstruction, denoising, and parameter mapping are becoming increasingly nonlinear, black-box, and at risk of "hallucination." These trends mean that traditional tools for judging confidence in an image (visual quality assessment, point-spread functions (PSFs), g-factor maps, etc.) are less helpful than before.

Region-optimized virtual (ROVir) coils: Localization and/or suppression of spatial regions using sensor-domain beamforming.

Purpose: In many MRI scenarios, magnetization is often excited from spatial regions that are not of immediate interest. Excitation of uninteresting magnetization can complicate the design of efficient imaging methods, leading to either artifacts or acquisitions that are longer than necessary. While there are many hardware- and sequence-based approaches for suppressing unwanted magnetization, this paper approaches this longstanding problem from a different and complementary angle, using beamforming to suppress signals from unwanted regions without modifying the acquisition hardware or pulse sequence.

BRAIN LESION DETECTION USING A ROBUST VARIATIONAL AUTOENCODER AND TRANSFER LEARNING.

Automated brain lesion detection from multi-spectral MR images can assist clinicians by improving sensitivity as well as specificity. Supervised machine learning methods have been successful in lesion detection. However, these methods usually rely on a large number of manually delineated images for specific imaging protocols and parameters and often do not generalize well to other imaging parameters and demographics.

A NETWORK-BASED APPROACH TO STUDY OF ADHD USING TENSOR DECOMPOSITION OF RESTING STATE FMRI DATA.

Identifying changes in functional connectivity in Attention Deficit Hyperactivity Disorder (ADHD) using functional magnetic resonance imaging (fMRI) can help us understand the neural substrates of this brain disorder. Many studies of ADHD using resting state fMRI (rs-fMRI) data have been conducted in the past decade with either manually crafted features that do not yield satisfactory performance, or automatically learned features that often lack interpretability. In this work, we present a tensor-based approach to identify brain networks and extract features from rs-fMRI data.

Robust autocalibrated structured low-rank EPI ghost correction.

Purpose: We propose and evaluate a new structured low-rank method for echo-planar imaging (EPI) ghost correction called Robust Autocalibrated LORAKS (RAC-LORAKS). The method can be used to suppress EPI ghosts arising from the differences between different readout gradient polarities and/or the differences between different shots. It does not require conventional EPI navigator signals, and is robust to imperfect autocalibration data.

Robust brain network identification from multi-subject asynchronous fMRI data.

We describe a novel method for robust identification of common brain networks and their corresponding temporal dynamics across subjects from asynchronous functional MRI (fMRI) using tensor decomposition. We first temporally align asynchronous fMRI data using the orthogonal BrainSync transform, allowing us to study common brain networks across sessions and subjects. We then map the synchronized fMRI data into a 3D tensor (vertices × time × subject/session).

Noise can speed backpropagation learning and deep bidirectional pretraining.

We show that the backpropagation algorithm is a special case of the generalized Expectation-Maximization (EM) algorithm for iterative maximum likelihood estimation. We then apply the recent result that carefully chosen noise can speed the average convergence of the EM algorithm as it climbs a hill of probability or log-likelihood. Then injecting such noise can speed the average convergence of the backpropagation algorithm for both the training and pretraining of multilayer neural networks.

Temporal non-local means filtering for studies of intrinsic brain connectivity from individual resting fMRI.

Characterizing functional brain connectivity using resting functional magnetic resonance imaging (fMRI) is challenging due to the relatively small Blood-Oxygen-Level Dependent contrast and low signal-to-noise ratio. Denoising using surface-based Laplace-Beltrami (LB) or volumetric Gaussian filtering tends to blur boundaries between different functional areas. To overcome this issue, a time-based Non-Local Means (tNLM) filtering method was previously developed to denoise fMRI data while preserving spatial structure.

Multidimensional correlation spectroscopic imaging of exponential decays: From theoretical principles to in vivo human applications.

Multiexponential modeling of relaxation or diffusion MR signal decays is a popular approach for estimating and spatially mapping different microstructural tissue compartments. While this approach can be quite powerful, it is also limited by the fact that one-dimensional multiexponential modeling is an ill-posed inverse problem with substantial ambiguities. In this article, we present an overview of a recent multidimensional correlation spectroscopic imaging approach to this problem.

Noise can speed Markov chain Monte Carlo estimation and quantum annealing.

Carefully injected noise can speed the average convergence of Markov chain Monte Carlo (MCMC) estimates and simulated annealing optimization. This includes quantum annealing and the MCMC special case of the Metropolis-Hastings algorithm. MCMC seeks the solution to a computational problem as the equilibrium probability density of a reversible Markov chain.

Noise-boosted bidirectional backpropagation and adversarial learning.

Bidirectional backpropagation trains a neural network with backpropagation in both the backward and forward directions using the same synaptic weights. Special injected noise can then improve the algorithm's training time and accuracy because backpropagation has a likelihood structure. Training in each direction is a form of generalized expectation-maximization because backpropagation itself is a form of generalized expectation-maximization.

Learning to define an electrical biomarker of the epileptogenic zone.

The role of fast activity as a potential biomarker in localization of the epileptogenic zone (EZ) remains controversial due to recently reported unsatisfactory performance. We recently identified a "fingerprint" of the EZ as a time-frequency pattern that is defined by a combination of preictal spike(s), fast oscillatory activity, and concurrent suppression of lower frequencies. Here we examine the generalizability of the fingerprint in application to an independent series of patients (11 seizure-free and 13 non-seizure-free after surgery) and show that the fingerprint can also be identified in seizures with lower frequency (such as beta) oscillatory activity.

Connectivity of the human insula: A cortico-cortical evoked potential (CCEP) study.

Objective: The human insula is increasingly being implicated as a multimodal functional network hub involved in a large variety of complex functions. Due to its inconspicuous location and highly vascular anatomy, it has historically been difficult to study. Cortico-cortical evoked potentials (CCEPs), utilize low frequency stimulation to map cerebral networks.

Anemia predicts lower white matter volume and cognitive performance in sickle and non-sickle cell anemia syndrome.

Severe chronic anemia is an independent predictor of overt stroke, white matter damage, and cognitive dysfunction in the elderly. Severe anemia also predisposes to white matter strokes in young children, independent of the anemia subtype. We previously demonstrated symmetrically decreased white matter (WM) volumes in patients with sickle cell disease (SCD).

THE FOURIER RADIAL ERROR SPECTRUM PLOT: A MORE NUANCED QUANTITATIVE EVALUATION OF IMAGE RECONSTRUCTION QUALITY.

In the modern biomedical image reconstruction literature, the quality of a reconstructed image is often numerically quantified using scalar error measures such as mean-squared error or the structural similarity index. While such measures provide a rough summary of image quality, they also suffer from well-known limitations. For example, a substantial amount of information is necessarily lost whenever the characteristics of a high-dimensional image are summarized by a single number.