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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Automated CT registration, segmentation, and quantification (AutoCT) v1.0

Processing and analyzing brain imaging is crucial in both scientific development and clinical field. In this software package, we build a pipeline that integrates automatic registration, segmentation, and quantitative analysis for subjects' CT scans. Leveraging diffeomorphic transformations, we enable optimized forward and inverse mappings between an image and the reference. Furthermore, we extract localized features from deformation field based on an online template process, which advances statistical learning downstream. The created templates, atlas as well as our methods provide the brain imaging community tools for AI implementations.

Essiari, Abdelilah↗
DOE OSTI2021

Automated CT registration, segmentation, and quantification (AutoCT) v1.1

Processing and analyzing brain imaging is crucial in both scientific development and clinical field. In this software package, we build a pipeline that integrates automatic registration, segmentation, and quantitative analysis for subjects' CT scans. Leveraging diffeomorphic transofrmations, we enable optimized forward and inverse mappings between an image and the reference. Furthermore, we extract localized features from deformation field based on an online template process, which advances statistical learning downstream. The created templates, atlas as well as our methods provide the brain imaging community tools for AI implementations

Bai, Zhe↗
DOE OSTI2022

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantum AI Based Enhanced Detection of Dementia

Quantum computing has the potential to significantly improve the early detection of Alzheimer's Disease and Related Dementias (ADRD). Quantum-enhanced machine learning can be used to perform an early screening of Alzheimer's disease using brain imaging data based on dataset of MRI scans from both healthy individuals and those diagnosed with Alzheimer's. This study aims to demonstrate the potential of quantum transfer learning to enhance the performance of the classical deep learning model for dementia detection. Using the MRI sagittal images available in the OASIS-2 (64 demented and 72 non-demented subjects between 60 and 96 years), we show how quantum techniques can transform a suboptimal classical model into a more effective solution for dementia detection, highlighting their potential impact on advancing healthcare technology. We begin with a simple classical deep learning model with a significantly smaller number of parameters, which gives suboptimal performance on the problem. Then, we apply different configurations of quantum transfer learning based on the pre-trained weak classifier (Figure 1). We fix the weak classifier's initial convolutional layers at their fixed pre-trained parameters and replace the last set of dense layers with a dressed quantum circuit (DQN), which we train to enhance performance. We performed 4-fold cross-validation for both the classical and the hybrid quantum models and trained them using Pennylane's `default.qubit' simulator and IonQ's Aria-1 simulator (noisy simulation). We showed that with significantly fewer parameters, the quantum transfer learning-based hybrid models showed significant performance enhancement over the base weak classical deep learning model for dementia detection. To classify between a demented and non-demented subject, the accuracy of quantum-based AI methods improved by 6 to 14% compared to classical methods. The sensitivity of the models improved by 4 to 17%. This shows that there are fewer chances of misclassifying demented patients. Figure 2 compares the performance of the hybrid quantum models and their base classical model, and Table 1 summarizes the results. We illustrated that with assistance from quantum machine learning, it is possible to enhance detection for dementia based on brain images. This shows the potential for practical utility of quantum computing in ADRD research.

Bhowmik, Sounak [University of Tennessee, Knoxvill↗
DOE OSTI2021

Breakthrough MEG Technology [Slides]

LANL technology is a disruptive innovation to change market dynamics. For medical imaging experts who want to rapidly diagnose brain disorders, our LANL breakthrough MEG solution delivers faster and easier brain imaging without having to go to major urban medical centers.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

An Oculometric Standard to Assess the Performance of the Ocular System for Long Duration Spaceflight

Changes in the human brain, due to spaceflight, have been a challenge to the space program since its inception; a challenge that is becoming more acute as extended International Space Station (ISS) missions become routine, a return to crewed lunar exploration is about to begin, and a multi-year crewed trip to Mars is being planned. Determining the extent to which neurophysiological adaptations may adversely impact performance in operational tasks, assessing the full-time course of these changes, and identifying/mitigating any potential long-term health consequences are crucial steps required to enable safe crew-autonomous, long-duration, deep-space missions. Vision is the predominant perceptual sense used to guide cognition and motor control in humans. Thus, it is critical for the success of any future, long-duration mission to understand how long-term exposure to microgravity and to other stressors of spaceflight and their interactions, impact visual function. This is an especially challenging task given the small and disparate samples from which we have been and will be able to collect human performance data. NASA has recently been carefully tracking spaceflight-induced ophthalmic changes, driven in large part by the fluid shifts related to microgravity. In particular, a recent study of Optical Coherence Tomography (OCT) postflight measures revealed that more than two-thirds of US crew members experience significant increases in retinal thickness after 6month or longer ISS missions. Space Associated Neuro-ocular Syndrome (SANS) also includes visual acuity decrements and other ocular structural changes that could adversely impact in-flight performance as missions become longer. However, the impact of spaceflight on the visual system is not limited to the retina. Recent comparisons of pre-and post-flight brain images have revealed structural changes throughout the brain that implicate visual, visuomotor, and visual-cognitive pathways, consistent with observed functional impacts (e.g., decreased speed/accuracy/timing of fine goal-oriented movements). Current limitations on inflight testing make it very difficult to determine when and under what conditions SANS and other disruptions of human neurological subsystems arise. Currently, one cannot anticipate the time course and extent of impairment and recovery. This study addresses this knowledge gap by creating an integrated framework of the relevant existing literature on visual and oculomotor function during spaceflight with an eye towards complementing current structural measures of visuomotor impairment with new oculometric standard measures. Using eye-movement based visual function assessment and diagnostics would provide a valuable enhancement of crew health and performance monitoring in support of deepspace exploration.

Vision↗
DOE OSTI2024

Tractometry of the Human Connectome Project: resources and insights

The Human Connectome Project (HCP) has become a keystone dataset in human neuroscience, with a plethora of important applications in advancing brain imaging methods and an understanding of the human brain. We focused on tractometry of HCP diffusion-weighted MRI (dMRI) data. We used an open-source software library (pyAFQ; https://yeatmanlab.github.io/pyAFQ) to perform probabilistic tractography and delineate the major white matter pathways in the HCP subjects that have a complete dMRI acquisition (n = 1,041). We used diffusion kurtosis imaging (DKI) to model white matter microstructure in each voxel of the white matter, and extracted tract profiles of DKI-derived tissue properties along the length of the tracts. We explored the empirical properties of the data: first, we assessed the heritability of DKI tissue properties using the known genetic linkage of the large number of twin pairs sampled in HCP. Second, we tested the ability of tractometry to serve as the basis for predictive models of individual characteristics (e.g., age, crystallized/fluid intelligence, reading ability, etc.), compared to local connectome features. To facilitate the exploration of the dataset we created a new web-based visualization tool and use this tool to visualize the data in the HCP tractometry dataset. Finally, we used the HCP dataset as a test-bed for a new technological innovation: the TRX file-format for representation of dMRI-based streamlines. We released the processing outputs and tract profiles as a publicly available data resource through the AWS Open Data program's Open Neurodata repository. We found heritability as high as 0.9 for DKI-based metrics in some brain pathways. We also found that tractometry extracts as much useful information about individual differences as the local connectome method. We released a new web-based visualization tool for tractometry—“Tractoscope” (https://nrdg.github.io/tractoscope). We found that the TRX files require considerably less disk space-a crucial attribute for large datasets like HCP. In addition, TRX incorporates a specification for grouping streamlines, further simplifying tractometry analysis.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Brain segmentation and the generation of cortical surfaces

This paper describes methods for white matter segmentation in brain images and the generation of cortical surfaces from the segmentations. We have developed a system that allows a user to start with a brain volume, obtained by modalities such as MRI or cryosection, and constructs a complete digital representation of the cortical surface. The methodology consists of three basic components: local parametric modeling and Bayesian segmentation; surface generation and local quadratic coordinate fitting; and surface editing. Segmentations are computed by parametrically fitting known density functions to the histogram of the image using the expectation maximization algorithm [DLR77]. The parametric fits are obtained locally rather than globally over the whole volume to overcome local variations in gray levels. To represent the boundary of the gray and white matter we use triangulated meshes generated using isosurface generation algorithms [GH95]. A complete system of local parametric quadratic charts [JWM+95] is superimposed on the triangulated graph to facilitate smoothing and geodesic curve tracking. Algorithms for surface editing include extraction of the largest closed surface. Results for several macaque brains are presented comparing automated and hand surface generation. Copyright 1999 Academic Press.

NASA Discipline Neuroscience↗
NASA NTRS2017

Spaceflight Effects on Neurocognitive Performance: Extent, Longevity and Neural Bases

We are conducting ongoing experiments in which we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre to post spaceflight. Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad ranging battery of sensory, motor, and cognitive assessments that are conducted pre flight, during flight, and post flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. Success in this endeavor would 1) result in identification of the underlying neural mechanisms and operational risks of spaceflight-induced changes in behavior, and 2) identify whether a return to normative behavioral function following re-adaptation to Earth's gravitational environment is associated with a restitution of brain structure and function or instead is supported by substitution with compensatory brain processes. We have collected data on several crewmembers and preliminary findings will be presented. Eventual comparison to results from our parallel bed rest study will enable us to parse out the multiple mechanisms contributing to any spaceflight-induced neural structural and behavioral changes that we observe.

Seidler, R. D.↗
NASA NTRS2017

Effects of One Year of Spaceflight on Neurocognitive Function

It is known that spaceflight adversely affects human sensorimotor function. With interests in longer duration deep space missions it is important to understand microgravity dose-response relationships. NASA's One Year Mission project allows for comparison of the effects of one year in space with those seen in more typical six month missions to the International Space Station. In the Neuromapping project we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre- to post-spaceflight. Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad-ranging battery of sensory, motor, and cognitive assessments that are conducted pre-flight, during flight, and post-flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. With the one year mission we had one crewmember participate in all of the same measures pre-, per- and post-flight as in our ongoing study. During this presentation we will provide an overview of the magnitude of changes observed with our brain and behavioral assessments for the one year crewmember in comparison to participants that have completed our six month study to date.

Seidler, R. D.↗
NASA NTRS2014

The Effects of Long Duration Head Down Tilt Bed Rest on Neurocognitive Performance: The Effects of Exercise Interventions

We are conducting ongoing experiments in which we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission and following 70 days exposure to a spaceflight analog, head down tilt bedrest. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre to post intervention (spaceflight, bedrest). Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad ranging battery of sensory, motor, and cognitive assessments that will be conducted pre flight, during flight, and post flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. Success in this endeavor would 1) result in identification of the underlying neural mechanisms and operational risks of spaceflight-induced changes in behavior, and 2) identify whether a return to normative behavioral function following re-adaptation to Earth's gravitational environment is associated with a restitution of brain structure and function or instead is supported by substitution with compensatory brain processes. Our ongoing bed rest participants are also engaging in exercise studies directed by Dr. Lori Ploutz Snyder. In this presentation, I will briefly highlight the existing literature linking exercise and fitness to brain and behavioral functions. I will also overview the metrics from my study that could be investigated in relation to the exercise and control subgroups.

Seidler, R. D.↗
NASA NTRS2014

The Effects of Spaceflight and a Spaceflight Analog on Neurocognitive Perfonnance: Extent, Longevity, and Neural Bases

We are conducting ongoing experiments in which we are performing structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations following a six month International Space Station mission and following 70 days exposure to a spaceflight analog, head down tilt bedrest. Our central hypothesis is that measures of brain structure, function, and network integrity will change from pre to post intervention (spaceflight, bedrest). Moreover, we predict that these changes will correlate with indices of cognitive, sensory, and motor function in a neuroanatomically selective fashion. Our interdisciplinary approach utilizes cutting edge neuroimaging techniques and a broad ranging battery of sensory, motor, and cognitive assessments that will be conducted pre flight, during flight, and post flight to investigate potential neuroplastic and maladaptive brain changes in crewmembers following long-duration spaceflight. Success in this endeavor would 1) result in identification of the underlying neural mechanisms and operational risks of spaceflight-induced changes in behavior, and 2) identify whether a return to normative behavioral function following re-adaptation to Earth's gravitational environment is associated with a restitution of brain structure and function or instead is supported by substitution with compensatory brain processes. With the bedrest study, we will be able to determine the neural and neurocognitive effects of extended duration unloading, reduced sensory inputs, and increased cephalic fluid distribution. This will enable us to parse out the multiple mechanisms contributing to any spaceflight-induced neural structural and behavioral changes that we observe in the flight study. In this presentation I will discuss preliminary results from six participants who have undergone the bed rest protocol. These individuals show decrements in balance and functional mobility, and alterations in brain structure and function, in association with extended bed rest.

Seidler, R. D.↗
NASA NTRS2016

Developing Personalized Sensorimotor Adaptability Countermeasures for Spaceflight

Astronauts experience sensorimotor disturbances during their initial exposure to microgravity and during the re-adaptation phase following a return to an Earth-gravitational environment. Interestingly, astronauts who return from spaceflight show substantial differences in their abilities to readapt to a gravitational environment. The ability to predict the manner and degree to which individual astronauts would be affected would improve the effectiveness of countermeasure training programs designed to enhance sensorimotor adaptability. In this paper we will be presenting results from our ground-based study that show how behavioral, brain imaging and genomic data may be used to predict individual differences in sensorimotor adaptability to novel sensorimotor environments. This approach will allow us to better design and implement sensorimotor adaptability training countermeasures against decrements in post-mission adaptive capability that are customized for each crewmember's sensory biases, adaptive capacity, brain structure, functional capacities, and genetic predispositions. The ability to customize adaptability training will allow more efficient use of crew time during training and will optimize training prescriptions for astronauts to ensure expected outcomes.

Mulavara, A. P.↗
NASA NTRS2017

Long Duration Head Down Tilt Bed Rest and Spaceflight Effects on Neurocognitive Performance: Extent, Longevity and Neural Bases

We have recently completed a long duration head down tilt bed rest (HDBR) study in which we performed structural and functional magnetic resonance brain imaging to identify the relationships between changes in neurocognitive function and neural structural alterations in a spaceflight analog environment. We are also collecting the same measures in crewmembers prior to and following a six month International Space Station mission. We will present data demonstrating that bed rest resulted in functional mobility and balance deterioration with recovery post-HDBR. We observed numerous changes in brain structure, function, and connectivity relative to a control group which were associated with pre to post bed rest changes in sensorimotor function. For example, gray matter volume (GMv) increased in posterior parietal areas and decreased in frontal regions. GMv increases largely overlapped with fluid decreases and vice versa. Larger increases in precentral gyrus (M1)/ postcentral gyrus (S1+2) GMv and fluid decreases were associated with smaller balance decrements. Vestibular activation in the bilateral insular cortex increased with bed rest and subsequently recovered. Larger increases in vestibular activation in multiple brain regions were associated with greater decrements in balance and mobility. We found connectivity increases between left M1 with right S1+2 and the superior parietal lobule, and right vestibular cortex with the cerebellum. Decreases were observed between right Lobule VIII with right S1+2 and the supramarginal gyrus, right posterior parietal cortex (PPC) with occipital regions, and the right superior posterior fissure with right Crus I and II. Connectivity strength between left M1 and right S1+2/superior parietal lobule increased the most in individuals that exhibited the least balance impairments. In sum, we observed HDBR-related changes in measures of brain structure, function, and network connectivity, which correlated with indices of sensorimotor function. Recovery was observed post HDBR but remained incomplete at 12 days post-HDBR. Preliminary findings from our parallel ongoing flight study will be compared and contrasted with bed rest results during this presentation.

Seidler, R. D.↗
NASA NTRS2003

Differences in the hemodynamic response to event-related motor and visual paradigms as measured by near-infrared spectroscopy

Several current brain imaging techniques rest on the assumption of a tight coupling between neural activity and hemodynamic response. The nature of this neurovascular coupling, however, is not completely understood. There is some evidence for a decoupling of these processes at the onset of neural activity, which manifests itself as a momentary increase in the relative concentration of deoxyhemoglobin (HbR). The existence of this early component of the hemodynamic response function, however, is controversial, as it is inconsistently found. Near infrared spectroscopy (NIRS) allows quantification of levels of oxyhemoglobin (HbO(2)) and HbR during task performance in humans. We acquired NIRS data during performance of simple motor and visual tasks, using rapid-presentation event-related paradigms. Our results demonstrate that rapid, event-related NIRS can provide robust estimates of the hemodynamic response without artifacts due to low-frequency signal components, unlike data from blocked designs. In both the motor and visual data the onset of the increase in HbO(2) occurs before HbR decreases, and there is a poststimulus undershoot. Our results also show that total blood volume (HbT) drops before HbO(2) and undershoots baseline, raising a new issue for neurovascular models. We did not find early deoxygenation in the motor data using physiologically plausible values for the differential pathlength factor, but did find one in the visual data. We suggest that this difference, which is consistent with functional magnetic resonance imaging (fMRI) data, may be attributable to different capillary transit times in these cortices.

NASA Program Biomedical Research and Countermeasur↗
DOE OSTI2022

Inference for Nonparanormal Partial Correlation via Regularized Rank-Based Nodewise Regression

Abstract Partial correlation is a common tool in studying conditional dependence for Gaussian distributed data. However, partial correlation being zero may not be equivalent to conditional independence under non-Gaussian distributions. In this paper, we propose a statistical inference procedure for partial correlations under the high-dimensional nonparanormal (NPN) model where the observed data are normally distributed after certain monotone transformations. The NPN partial correlation is the partial correlation of the normal transformed data under the NPN model, which is a more general measure of conditional dependence. We estimate the NPN partial correlations by regularized nodewise regression based on the empirical ranks of the original data. A multiple testing procedure is proposed to identify the nonzero NPN partial correlations. The proposed method can be carried out by a simple coordinate descent algorithm for lasso optimization. It is easy-to-implement and computationally more efficient compared to the existing methods for estimating NPN graphical models. Theoretical results are developed to show the asymptotic normality of the proposed estimator and to justify the proposed multiple testing procedure. Numerical simulations and a case study on brain imaging data demonstrate the utility of the proposed procedure and evaluate its performance compared to the existing methods. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

WiDS Livermore Datathon 2025

The WiDS Datathon 2025 requires participants to build a model to predict both an individual’s sex and their ADHD diagnosis using functional brain imaging data of children and adolescents and their socio-demographic, emotions, and parenting information. The task is to create a multi-outcome model to predict two target variables: 1) ADHD (1=yes or 0=no) and 2) female (1=yes or 0=no).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain: The Acute to Chronic Pain Signatures (A2CPS) Study Protocol

Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or “omics,” quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.

60 APPLIED LIFE SCIENCES↗