A5057244887- Advanced Neuroimaging Techniques and Applications
- Advanced MRI Techniques and Applications
- Functional Brain Connectivity Studies
- Visual perception and processing mechanisms
- Retinal Imaging and Analysis
- Neural dynamics and brain function
- Scientific Computing and Data Management
- MRI in cancer diagnosis
- Neuroscience and Neural Engineering
- EEG and Brain-Computer Interfaces
- Advanced Memory and Neural Computing
- Bone and Joint Diseases
- Cell Image Analysis Techniques
- Fetal and Pediatric Neurological Disorders
- Photoreceptor and optogenetics research
- Glaucoma and retinal disorders
- Neural and Behavioral Psychology Studies
- Neonatal and fetal brain pathology
- Retinal Diseases and Treatments
- Memory and Neural Mechanisms
- Optical Coherence Tomography Applications
- Neuroscience and Neuropharmacology Research
- Medical Imaging Techniques and Applications
- Computational Physics and Python Applications
- Biomedical and Engineering Education
University of Washington
2016-2025
Stanford University
2012-2025
World Institute on Disability
2024-2025
Seattle University
2015-2023
Institut des Sciences Cognitives Marc Jeannerod
2021
Middle East Technical University
2021
Behavioral Tech Research, Inc.
2015-2019
University of California, Berkeley
2009-2019
Carnegie Mellon University
2019
Washington Research Foundation
2018
The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens thousands studies using such as functional MRI and diffusion weighted have allowed for the non-invasive study brain. Despite fact that is routinely used to obtain data neuroscience research, there been no widely adopted standard organizing describing collected in an experiment. This renders sharing reusing (within or between labs) difficult if not impossible unnecessarily...
Diffusion Imaging in Python (Dipy) is a free and open source software projectfor the analysis of data from diffusion magnetic resonance imaging (dMRI)experiments. dMRI an application MRI that can be used to measurestructural features brain white matter. Many methods have been developed touse model local configuration matter nerve fiberbundles infer trajectory bundles connecting different parts thebrain.Dipy gathers implementations many dMRI, including:diffusion signal pre-processing;...
The neural mechanisms underlying cognitive deficits in schizophrenia remain essentially unknown. GABA hypothesis proposes that reduced neuronal concentration and neurotransmission results impairments schizophrenia. However, few vivo studies have directly examined this hypothesis. We used magnetic resonance spectroscopy (MRS) at high field to measure visual cortical levels 13 subjects with demographically matched healthy control subjects. found the group had an approximately 10% reduction...
Evaluation of clinical images is essential for diagnosis in many specialties.Therefore the development computer vision algorithms to help analyze biomedical will be important.In ophthalmology, optical coherence tomography (OCT) critical managing retinal conditions.We developed a convolutional neural network (CNN) that detects intraretinal fluid (IRF) on OCT manner indistinguishable from clinicians.Using 1,289 images, CNN segmented with 0.911 cross-validated Dice coefficient, compared...
Significance The vertical occipital fasciculus (VOF) is a major white-matter fascicle connecting dorsal and ventral visual cortex. Few vision scientists or cognitive neuroscientists are aware of the VOF's existence. scarcity papers on this important pathway stems from contentious history surrounding its discovery by Wernicke in 1881. We review conflict classic, postmortem, VOF measurements, we introduce modern, vivo methods to precisely characterize cortical terminations unique tissue...
In task-based functional magnetic resonance imaging (fMRI), researchers seek to measure fMRI signals related a given task or condition. many circumstances, measuring this signal of interest is limited by noise. study, we present GLMdenoise, technique that improves signal-to-noise ratio (SNR) entering noise regressors into general linear model (GLM) analysis data. The are derived conducting an initial fit determine voxels unrelated the experimental paradigm, performing principal components...
Human visual cortex comprises many field maps organized into clusters. A standard organization separates 2 distinct clusters within ventral and dorsal cortex. We combined fMRI, diffusion MRI, fiber tractography to identify a major white matter pathway, the vertical occipital fasciculus (VOF), connecting use model-based method assess statistical evidence supporting several aspects of VOF wiring pattern. There is strong hypothesis that communicate through VOF. The cortical projection zones...
Abstract White matter tissue properties are known to correlate with performance across domains ranging from reading math, executive function. Here, we use a longitudinal intervention design examine experience-dependent growth in skills and white grade school-aged, struggling readers. Diffusion MRI data were collected at regular intervals during an 8-week, intensive intervention. These measurements reveal large-scale changes throughout collection of tracts, concert skill. Additionally,...
Although damage to the primary visual cortex (V1) causes hemianopia, many patients retain some residual vision; known as blindsight. We show that blindsight may be facilitated by an intact white-matter pathway between lateral geniculate nucleus and motion area hMT+. Visual psychophysics, diffusion-weighted magnetic resonance imaging fibre tractography were applied in 17 with V1 acquired during adulthood 9 age-matched controls. Individuals subdivided into positive (preserved vision) negative...
Purpose: To determine if deep learning networks could be trained to forecast a future 24-2 Humphrey Visual Field (HVF). Participants: All patients who obtained HVF at the University of Washington. Methods: datapoints from consecutive HVFs 1998 2018 were extracted Washington database. Ten-fold cross validation with held out test set was used develop three main phases model development: architecture selection, dataset combination and time-interval training transfer learning, train artificial...
Poster presented at SIAM CSE17 PP108 Minisymposterium: Software Productivity and Sustainability for CSE Data ScienceAbstract:This poster describes the motivation progress of Journal Open Source (JOSS), a free, open-access journal designed to publish brief papers about research software. The primary purpose JOSS is enable developers software receive citation credit equivalent typical archival publications. are deliberately extremely short, required include short abstract describing...
Abstract Degenerative retinal diseases such as retinitis pigmentosa and macular degeneration cause irreversible vision loss in more than 10 million people worldwide. Retinal prostheses, now implanted over 250 patients worldwide, electrically stimulate surviving cells order to evoke neuronal responses that are interpreted by the brain visual percepts (‘phosphenes’). However, instead of seeing focal spots light, current implant users perceive highly distorted phosphenes vary shape both across...
Visual neuroscientists have discovered fundamental properties of neural representation through careful analysis responses to controlled stimuli. Typically, different are studied and modeled separately. To integrate our knowledge, it is necessary build general models that begin with an input image predict a wide range In this study, we develop model accepts arbitrary band-pass grayscale as predicts blood oxygenation level dependent (BOLD) in early visual cortex output. The has cascade...
Abstract Tractography has created new horizons for researchers to study brain connectivity in vivo. However, tractography is an advanced and challenging method that not been used so far medical data analysis at a large scale comparison other traditional imaging methods. This work allows be high-quality analytics. BUndle ANalytics (BUAN) fast, robust, flexible computational framework real-world tractometric studies. BUAN combines anatomical information analyze the datasets identifies...
Models of diffusion MRI within a voxel are useful for making inferences about the properties tissue and inferring fiber orientation distribution used by tractography algorithms. A model must fit data accurately. However, evaluations model-accuracy commonly models have not been published before. Here, we evaluate two main classes models. The tensor (DTM) summarizes as 3-dimensional Gaussian distribution. Sparse fascicle (SFM) summarize signal sum signals originating from collection fascicles...
Abstract Despite advances in artificial intelligence (AI), its application medical imaging has been burdened and limited by expert-generated labels. We used images from optical coherence tomography angiography (OCTA), a relatively new modality that measures retinal blood flow, to train an AI algorithm generate flow maps standard (OCT) images, exceeding the ability bypassing need for expert labeling. Deep learning was able infer single structural OCT with similar fidelity OCTA significantly...
Cross-sectional studies have linked differences in white matter tissue properties to reading skills. However, past reported a range of, sometimes conflicting, results. Some suggest that act as individual-level traits predictive of skill, whereas others skill and develop function an individual's educational experience. In the present study, we tested two hypotheses: a) diffusion reflect stable brain characteristics relate individual ability or b) is dynamic system, with learning over time. To...
Abstract Head motion correction is particularly challenging in diffusion‐weighted MRI (dMRI) scans due to the dramatic changes image contrast at different gradient strengths and directions. typically performed using a Gaussian Process model implemented FSL's Eddy. Recently, 3dSHORE‐based SHORELine method was introduced that does not require shell‐based acquisitions, but it has been previously benchmarked. Here we perform comprehensive evaluation of both methods on realistic simulations...
Abstract Past studies leveraging cross-sectional data have raised questions surrounding the relationship between diffusion properties of white matter and academic skills. Some suggested that serve as static predictors skills, whereas other observed no such relationship. On hand, longitudinal within-individual changes in are linked to learning gains over time. In present study, we look replicate extend previous results linking left arcuate fasciculus individual differences reading...
Visual perception of a stimulus is function the visual context in which it displayed. Surround suppression specific form contextual modulation whereby perceived contrast center decreased by high-contrast surround. Recent studies have demonstrated that individuals with schizophrenia are less prone to effects, suggesting impairments cortical lateral connectivity. We tested whether altered orientation selective. Participants viewed an annulus consisting contrast-reversing sinusoidal gratings...