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Thomas Ernst

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13 papers

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YNIMG Journal 2020 Journal Article

Prospective motion correction of fMRI: Improving the quality of resting state data affected by large head motion

Danilo Maziero
Carlo Rondinoni
Theo Marins
Victor Andrew Stenger
Thomas Ernst

The quality of functional MRI (fMRI) data is affected by head motion. It has been shown that fMRI data quality can be improved by prospectively updating the gradients and radio-frequency pulses in response to head motion during image acquisition by using an MR-compatible optical tracking system (prospective motion correction, or PMC). Recent studies showed that PMC improves the temporal Signal to Noise Ratio (tSNR) of resting state fMRI data (rs-fMRI) acquired from subjects not moving intentionally. Besides that, the time courses of Independent Components (ICs), resulting from Independent Component Analysis (ICA), were found to present significant temporal correlation with the motion parameters recorded by the camera. However, the benefits of applying PMC for improving the quality of rs-fMRI acquired under large head movements and its effects on resting state networks (RSN) and connectivity matrices are still unknown. In this study, subjects were instructed to cross their legs at will while rs-fMRI data with and without PMC were acquired, which generated head motion velocities ranging from 4 to 30 mm/s. We also acquired fMRI data without intentional motion. Independent component analysis of rs-fMRI was performed to evaluate IC maps and time courses of RSNs. We also calculated the temporal correlation among different brain regions and generated connectivity matrices for the different motion and PMC conditions. In our results we verified that the crossing leg movements reduced the tSNR of sessions without and with PMC by 45 and 20%, respectively, when compared to sessions without intentional movements. We have verified an interaction between head motion speed and PMC status, showing stronger attenuation of tSNR for acquisitions without PMC than for those with PMC. Additionally, the spatial definition of major RSNs, such as default mode, visual, left and right central executive networks, was improved when PMC was enabled. Furthermore, motion altered IC-time courses by decreasing power at low frequencies and increasing power at higher frequencies (typically associated with artefacts). PMC partially reversed these alterations of the power spectra. Finally, we showed that PMC provides temporal correlation matrices for data acquired under motion conditions more comparable to those obtained by fMRI sessions where subjects were instructed not to move.

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YNIMG Journal 2019 Journal Article

Image processing and analysis methods for the Adolescent Brain Cognitive Development Study

Donald J. Hagler
SeanN. Hatton
M. Daniela Cornejo
Carolina Makowski
Damien A. Fair
Anthony Steven Dick
Matthew T. Sutherland
B.J. Casey

The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing, nationwide study of the effects of environmental influences on behavioral and brain development in adolescents. The main objective of the study is to recruit and assess over eleven thousand 9-10-year-olds and follow them over the course of 10 years to characterize normative brain and cognitive development, the many factors that influence brain development, and the effects of those factors on mental health and other outcomes. The study employs state-of-the-art multimodal brain imaging, cognitive and clinical assessments, bioassays, and careful assessment of substance use, environment, psychopathological symptoms, and social functioning. The data is a resource of unprecedented scale and depth for studying typical and atypical development. The aim of this manuscript is to describe the baseline neuroimaging processing and subject-level analysis methods used by ABCD. Processing and analyses include modality-specific corrections for distortions and motion, brain segmentation and cortical surface reconstruction derived from structural magnetic resonance imaging (sMRI), analysis of brain microstructure using diffusion MRI (dMRI), task-related analysis of functional MRI (fMRI), and functional connectivity analysis of resting-state fMRI. This manuscript serves as a methodological reference for users of publicly shared neuroimaging data from the ABCD Study.

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YNIMG Journal 2017 Journal Article

Mapping the critical gestational age at birth that alters brain development in preterm-born infants using multi-modal MRI

Dan Wu
Linda Chang
Kentaro Akazawa
Kumiko Oishi
Jon Skranes
Thomas Ernst
Kenichi Oishi

Preterm birth adversely affects postnatal brain development. In order to investigate the critical gestational age at birth (GAB) that alters the developmental trajectory of gray and white matter structures in the brain, we investigated diffusion tensor and quantitative T2 mapping data in 43 term-born and 43 preterm-born infants. A novel multivariate linear model—the change point model, was applied to detect change points in fractional anisotropy, mean diffusivity, and T2 relaxation time. Change points captured the “critical” GAB value associated with a change in the linear relation between GAB and MRI measures. The analysis was performed in 126 regions across the whole brain using an atlas-based image quantification approach to investigate the spatial pattern of the critical GAB. Our results demonstrate that the critical GABs are region- and modality-specific, generally following a central-to-peripheral and bottom-to-top order of structural development. This study may offer unique insights into the postnatal neurological development associated with differential degrees of preterm birth.

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YNIMG Journal 2016 Journal Article

Probabilistic maps of the white matter tracts with known associated functions on the neonatal brain atlas: Application to evaluate longitudinal developmental trajectories in term-born and preterm-born infants

Kentaro Akazawa
Linda Chang
Robyn Yamakawa
Sara Hayama
Steven Buchthal
Daniel Alicata
Tamara Andres
Deborrah Castillo

Diffusion tensor imaging (DTI) has been widely used to investigate the development of the neonatal and infant brain, and deviations related to various diseases or medical conditions like preterm birth. In this study, we created a probabilistic map of fiber pathways with known associated functions, on a published neonatal multimodal atlas. The pathways-of-interest include the superficial white matter (SWM) fibers just beneath the specific cytoarchitectonically defined cortical areas, which were difficult to evaluate with existing DTI analysis methods. The Jülich cytoarchitectonic atlas was applied to define cortical areas related to specific brain functions, and the Dynamic Programming (DP) method was applied to delineate the white matter pathways traversing through the SWM. Probabilistic maps were created for pathways related to motor, somatosensory, auditory, visual, and limbic functions, as well as major white matter tracts, such as the corpus callosum, the inferior fronto-occipital fasciculus, and the middle cerebellar peduncle, by delineating these structures in eleven healthy term-born neonates. In order to characterize maturation-related changes in diffusivity measures of these pathways, the probabilistic maps were then applied to DTIs of 49 healthy infants who were longitudinally scanned at three time-points, approximately five weeks apart. First, we investigated the normal developmental pattern based on 19 term-born infants. Next, we analyzed 30 preterm-born infants to identify developmental patterns related to preterm birth. Last, we investigated the difference in diffusion measures between these groups to evaluate the effects of preterm birth on the development of these functional pathways. Term-born and preterm-born infants both demonstrated a time-dependent decrease in diffusivity, indicating postnatal maturation in these pathways, with laterality seen in the corticospinal tract and the optic radiation. The comparison between term- and preterm-born infants indicated higher diffusivity in the preterm-born infants than in the term-born infants in three of these pathways: the body of the corpus callosum; the left inferior longitudinal fasciculus; and the pathway connecting the left primary/secondary visual cortices and the motion-sensitive area in the occipitotemporal visual cortex (V5/MT+). Probabilistic maps provided an opportunity to investigate developmental changes of each white matter pathway. Whether alterations in white matter pathways can predict functional outcomes will be further investigated in a follow-up study.

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YNIMG Journal 2014 Journal Article

A Bayesian approach to the creation of a study-customized neonatal brain atlas

Yajing Zhang
Linda Chang
Can Ceritoglu
Jon Skranes
Thomas Ernst
Susumu Mori
Michael I. Miller
Kenichi Oishi

Atlas-based image analysis (ABA), in which an anatomical “parcellation map” is used for parcel-by-parcel image quantification, is widely used to analyze anatomical and functional changes related to brain development, aging, and various diseases. The parcellation maps are often created based on common MRI templates, which allow users to transform the template to target images, or vice versa, to perform parcel-by-parcel statistics, and report the scientific findings based on common anatomical parcels. The use of a study-specific template, which represents the anatomical features of the study population better than common templates, is preferable for accurate anatomical labeling; however, the creation of a parcellation map for a study-specific template is extremely labor intensive, and the definitions of anatomical boundaries are not necessarily compatible with those of the common template. In this study, we employed a volume-based template estimation (VTE) method to create a neonatal brain template customized to a study population, while keeping the anatomical parcellation identical to that of a common MRI atlas. The VTE was used to morph the standardized parcellation map of the JHU-neonate-SS atlas to capture the anatomical features of a study population. The resultant “study-customized” T1-weighted and diffusion tensor imaging (DTI) template, with three-dimensional anatomical parcellation that defined 122 brain regions, was compared with the JHU-neonate-SS atlas, in terms of the registration accuracy. A pronounced increase in the accuracy of cortical parcellation and superior tensor alignment were observed when the customized template was used. With the customized atlas-based analysis, the fractional anisotropy (FA) detected closely approximated the manual measurements. This tool provides a solution for achieving normalization-based measurements with increased accuracy, while reporting scientific findings in a consistent framework.

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YNIMG Journal 2014 Journal Article

Simultaneous Multi-Slice fMRI using spiral trajectories

Benjamin Zahneisen
Benedikt A. Poser
Thomas Ernst
Andrew V. Stenger

Parallel imaging methods using multi-coil receiver arrays have been shown to be effective for increasing MRI acquisition speed. However parallel imaging methods for fMRI with 2D sequences show only limited improvements in temporal resolution because of the long echo times needed for BOLD contrast. Recently, Simultaneous Multi-Slice (SMS) imaging techniques have been shown to increase fMRI temporal resolution by factors of four and higher. In SMS fMRI multiple slices can be acquired simultaneously using Echo Planar Imaging (EPI) and the overlapping slices are un-aliased using a parallel imaging reconstruction with multiple receivers. The slice separation can be further improved using the “blipped-CAIPI” EPI sequence that provides a more efficient sampling of the SMS 3D k-space. In this paper a blipped-spiral SMS sequence for ultra-fast fMRI is presented. The blipped-spiral sequence combines the sampling efficiency of spiral trajectories with the SMS encoding concept used in blipped-CAIPI EPI. We show that blipped spiral acquisition can achieve almost whole brain coverage at 3mm isotropic resolution in 168ms. It is also demonstrated that the high temporal resolution allows for dynamic BOLD lag time measurement using visual/motor and retinotopic mapping paradigms. The local BOLD lag time within the visual cortex following the retinotopic mapping stimulation of expanding flickering rings is directly measured and easily translated into an eccentricity map of the cortex.

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YNIMG Journal 2011 Journal Article

Multi-contrast human neonatal brain atlas: Application to normal neonate development analysis

Kenichi Oishi
Susumu Mori
Pamela K. Donohue
Thomas Ernst
Lynn Anderson
Steven Buchthal
Andreia Faria
Hangyi Jiang

MRI is a sensitive method for detecting subtle anatomic abnormalities in the neonatal brain. To optimize the usefulness for neonatal and pediatric care, systematic research, based on quantitative image analysis and functional correlation, is required. Normalization-based image analysis is one of the most effective methods for image quantification and statistical comparison. However, the application of this methodology to neonatal brain MRI scans is rare. Some of the difficulties are the rapid changes in T1 and T2 contrasts and the lack of contrast between brain structures, which prohibits accurate cross-subject image registration. Diffusion tensor imaging (DTI), which provides rich and quantitative anatomical contrast in neonate brains, is an ideal technology for normalization-based neonatal brain analysis. In this paper, we report the development of neonatal brain atlases with detailed anatomic information derived from DTI and co-registered anatomical MRI. Combined with a diffeomorphic transformation, we were able to normalize neonatal brain images to the atlas space and three-dimensionally parcellate images into 122 regions. The accuracy of the normalization was comparable to the reliability of human raters. This method was then applied to babies of 37–53 post-conceptional weeks to characterize developmental changes of the white matter, which indicated a posterior-to-anterior and a central-to-peripheral direction of maturation. We expect that future applications of this atlas will include investigations of the effect of prenatal events and the effects of preterm birth or low birth weights, as well as clinical applications, such as determining imaging biomarkers for various neurological disorders.

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YNIMG Journal 2011 Journal Article

Phase contrast imaging in neonates

Kai Zhong
Thomas Ernst
Steve Buchthal
Oliver Speck
Lynn Anderson
Linda Chang

Magnetic resonance phase images can yield superior gray and white matter contrast compared to conventional magnitude images. However, the underlying contrast mechanisms are not yet fully understood. Previous studies have been limited to high field acquisitions in adult volunteers and patients. In this study, phase imaging in the neonatal brain is demonstrated for the first time. Compared to adults, phase differences between gray and white matter are significantly reduced but not inverted in neonates with little myelination and iron deposits in their brains. The remaining phase difference between the neonatal and adult brains may be due to a different macromolecule concentration in the unmyelinated brain of the neonates and thus a different frequency due to water macromolecule exchange. Additionally, the susceptibility contrast from brain myelination can be separately studied in neonates during brain development. Therefore, magnetic resonance phase imaging is suggested as a novel tool to study neonatal brain development and pathologies in neonates.

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YNIMG Journal 2008 Journal Article

Decreased brain dopamine transporters are related to cognitive deficits in HIV patients with or without cocaine abuse

Linda Chang
Gene-Jack Wang
Nora D. Volkow
Thomas Ernst
Frank Telang
Jean Logan
Joanna S. Fowler

Objective Decreased dopamine transporters (DAT) in the basal ganglia were shown in patients with human immunodeficiency virus (HIV) associated dementia. Therefore, we assessed the relationship between striatal DAT and dopamine D2 receptors (D2R) availability and cognitive performance, and whether cocaine abuse, a common co-morbid condition in HIV patients, would be associated with further decreases in DAT and D2 receptors. Methods 35 HIV-positive subjects [24 without (HIV) and 11 with a history of cocaine-dependence (HIV+Coc)] and 14 seronegative controls (SN) were evaluated with PET to measure DAT using [C-11]cocaine and D2R using [C-11]raclopride (availability of DAT or D2R estimated with Bmax/Kd), and a battery of neuropsychological tests. Results Compared to SN controls, both HIV subject groups had lower DAT in putamen (HIV+Coc: − 16. 7%, p = 0. 003; HIV: − 12. 2%, p = 0. 02) and only HIV+Coc showed lower DAT in caudate (− 12. 2%, p = 0. 04). Lower D2R in both regions of both HIV groups were accounted by the greater nicotine use. Lower DAT, but not D2R, in putamen and caudate were associated with poorer performance on multiple neuropsychological tests, corrected for the effects of age, education, intelligence, mood, and nicotine use. Furthermore, a structural equation model (SEM) indicated that lower average dopamine function (both DAT and D2R) were related to poorer overall function on neuropsychological tests (p = 0. 05). Interpretation Reduced dopaminergic function may contribute to cognitive dysfunction in HIV patients with or without additional cocaine abuse. These findings suggest that these HIV patients may benefit from treatments that enhance dopamine function or protection from dopamine cell injury.

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YNIMG Journal 2005 Journal Article

The effect of small rotations on R2* measured with echo planar imaging

Elisabeth C. Caparelli
Dardo Tomasi
Thomas Ernst

Several modern MRI techniques, such as functional MRI (fMRI), rely on the detection of microscopic changes in magnetic susceptibility. However, differences in magnetic susceptibility between brain tissue, bone, and air also produce local magnetic field gradients that may interfere with the contrast of interest, particularly at high field strengths. Since the magnetic field distribution depends on the orientation of the human head in the MRI scanner, head rotations can change the effective transverse relaxation rate (R 2*) and confound fMRI studies. The size of the R 2* changes produced by small head rotations was estimated from a brain-shaped gel-phantom at 4 T, by measuring the signal decay at 96 different echo times. Similar measurements were carried out in a human study. Rotations larger than 2° changed R 2* more than 1. 5 Hz in the phantom, and indicate that even small rotations may compromise fMRI results.

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YNIMG Journal 2004 Journal Article

Regional patterns of brain metabolites in AIDS dementia complex

Constantin T. Yiannoutsos
Thomas Ernst
Linda Chang
P. Lani Lee
Todd Richards
Christina M. Marra
Dieter J. Meyerhoff
Jeffrey G. Jarvik

The relationship of the cellular changes in the HIV-infected brain to the onset and progression of AIDS dementia complex (ADC) remains uncertain. We undertook an in vivo proton magnetic resonance spectroscopy (MRS) study and used factor analysis to identify specific cellular and regional brain changes that may serve as metabolic markers of ADC. The ratio of N-acetyl aspartate (NAA), choline (Cho), and myoinositol (MI) over creatine (Cr), markers of neuronal and glial cell metabolism, were measured in the basal ganglia, centrum semiovale, and parietal cortex from 100 subjects with and without ADC. Three metabolic patterns were identified, which we termed “inflammatory” (mainly MI/Cr elevations in all three regions plus Cho/Cr increases in the centrum semiovale and parietal cortex), “basal ganglia” (mostly NAA/Cr and Cho/Cr elevations in the basal ganglia), and “neuronal” (primarily NAA/Cr reductions in the centrum semiovale and the parietal cortex). Logistic regression analysis revealed that, adjusted for age, basal ganglia and neuronal pattern scores were strongly associated with ADC but inflammatory levels were not. We conclude that by using factor analysis, we are able to combine multiple metabolites across brain regions in a biologically plausible manner and construct a predictive model of ADC adjusting for relevant factors such as age.

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YNIMG Journal 2003 Journal Article

k-Space based summary motion detection for functional magnetic resonance imaging

Elisabeth C. Caparelli
Dardo Tomasi
Sheeba Arnold
Linda Chang
Thomas Ernst

Functional MRI studies are very sensitive to motion; head movements of as little as 1-mm translations or 1° rotations may cause spurious signals. An algorithm was developed that uses k-space MRI data to monitor subject motion during functional MRI time series. A k-space weighted average of squared difference between the initial scan and subsequent scans is calculated, which summarizes subject motion in a single quality parameter; however, the quality parameter cannot be used for motion correction. The evolution of this quality parameter throughout a time series indicates whether head motion is within a predetermined limit. Fifty functional MRI studies were used to calibrate the sensitivity of the algorithm, using the six rigid-body registration parameters (three translations and three rotations) from the statistical parametric mapping (SPM99) package as a reference. The average correlation coefficient between the new quality parameter and the reference value from SPM was 0. 84. The simple algorithm correctly classified acceptable or excessive motion with 90% accuracy, with the remaining 10% being borderline cases. This method makes it possible to evaluate brain motion within seconds after a scan and to decide whether a study needs to be repeated.

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YNIMG Journal 2002 Journal Article

Relationships among Brain Metabolites, Cognitive Function, and Viral Loads in Antiretroviral-Naı̈ve HIV Patients

Linda Chang
Thomas Ernst
Mallory D Witt
Nina Ames
Megan Gaiefsky
Eric Miller

This study aims to determine the relationship among cerebral metabolite concentrations (on proton magnetic resonance spectroscopy or 1H MRS), cognitive function, and clinical variables (CD4, plasma and CSF viral loads, and lipids) in antiretroviral medication-naı̈ve HIV patients. We hypothesized that the probable glial markers myo-inositol [MI] and choline compounds [CHO] would correlate with cognitive function, CD4 count, and viral loads, but not with serum lipids. Forty-five antiretroviral-drug-naı̈ve HIV patients and 25 control subjects were evaluated. Frontal lobe [MI], [CHO], and total creatine [CR] were elevated, while basal ganglia [CR] were decreased, with increasing dementia severity. As a group, HIV patients showed slowing on fine motor (Grooved Pegboard) and psychomotor function (Trails A & B), and deficits on executive function (Stroop tasks). Lower CD4 counts and elevated plasma viral loads were associated with elevated frontal white matter [MI], which in turn correlated with the Stroop tasks. These findings suggest that systemic factors (resulting from suppressed immune function and higher plasma viral load) may lead to glial proliferation (elevated [MI], [CHO], and [CR]) in the frontal white matter, which in turn may contribute to deficits on executive function in HIV. Studying antiretroviral-naı̈ve patients minimized the confounding effects of antiretroviral treatment on the clinical, MRS, and neuropsychological variables, and allowed for a more accurate assessment of the relationships among these measurements. Metabolite concentrations, rather than metabolite ratios, should be measured since [CR], a commonly used reference for metabolite ratios, varies with disease severity in both frontal lobe and basal ganglia.

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