Jonathan R Polimeni

Jonathan R Polimeni
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Jonathan verified their affiliation via an institutional email.
Verified
Jonathan verified their affiliation via an institutional email.
  • Ph.D.
  • Professor (Associate) at Stanford University

About

276
Publications
65,180
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26,963
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Introduction
Jonathan R Polimeni currently works in the Department of Radiology at Stanford University. Jonathan does research in Neuroscience and functional MRI.
Current institution
Stanford University
Current position
  • Professor (Associate)
Additional affiliations
February 2007 - present
Massachusetts General Hospital
Position
  • Professor (Assistant)
February 2007 - July 2023
Harvard Medical School
Position
  • Professor (Assistant)
February 2007 - present
Harvard Medical School
Position
  • Professor (Assistant)

Publications

Publications (276)
Preprint
Full-text available
Sleep entails significant changes in cerebral hemodynamics and metabolism. Yet, the way these processes evolve throughout wakefulness and sleep and their spatiotemporal dependence remain largely unknown. Here, by integrating a novel functional PET technique with simultaneous EEG-fMRI, we reveal a tightly coupled temporal progression of global hemod...
Article
Full-text available
In functional magnetic resonance imaging (fMRI), neural activity is inferred from the associated hemodynamic response. However, the degree to which hemodynamics can track dynamic changes in neuronal activity, and thus the ultimate temporal resolution of fMRI, remains unknown. To evaluate the detectability of stimulus-driven high-frequency blood oxy...
Article
Full-text available
In graph theory, “multilayer networks” represent systems involving several interconnected topological levels. One example in neuroscience is the stratification of connections between different cortical depths or “laminae,” which is becoming noninvasively accessible in humans using ultrahigh-resolution functional MRI (fMRI). Here, we applied a multi...
Preprint
Full-text available
Over the past two decades, rapid advancements in magnetic resonance technology have significantly enhanced the imaging resolution of functional Magnetic Resonance Imaging (fMRI), far surpassing its initial capabilities. Beyond mapping brain functional architecture at unprecedented scales, high-spatial-resolution acquisitions have also inspired and...
Article
Full-text available
The ability to detect fast responses with functional MRI depends on the speed of hemodynamic responses to neural activity, because hemodynamic responses act as a temporal low-pass filter which blurs rapid changes. However, the shape and timing of hemodynamic responses are highly variable across the brain and across stimuli. This heterogeneity of re...
Article
Full-text available
Purpose To overcome the major challenges in diffusion MRI (dMRI) acquisition, including limited SNR, distortion/blurring, and susceptibility to motion artifacts. Theory and Methods A novel Romer‐EPTI technique is developed to achieve SNR‐efficient acquisition while providing distortion‐free imaging, minimal spatial blurring, high motion robustness...
Preprint
Full-text available
Functional Positron Emission Tomography (fPET) with (bolus plus) constant infusion of [18F]-fluorodeoxyglucose FDG), known as fPET-FDG, is a recently introduced technique in human neuroimaging, enabling the detection of dynamic glucose metabolism changes within a single scan. However, the statistical analysis of fPET-FDG data remains challenging be...
Article
Full-text available
Purpose To develop a single‐shot SNR‐efficient distortion‐free multi‐echo imaging technique for dynamic imaging applications. Methods Echo planar time‐resolved imaging (EPTI) was first introduced as a multi‐shot technique for distortion‐free multi‐echo imaging. This work aims to develop single‐shot EPTI (ss‐EPTI) to achieve improved robustness to...
Article
Full-text available
Macrovascular biases have been a long-standing challenge for functional magnetic resonance imaging (fMRI), limiting its ability to detect spatially specific neural activity. Recent experimental studies, including our own, found substantial resting-state macrovascular blood-oxygenation level-dependent (BOLD) fMRI contributions from large veins and a...
Article
Full-text available
Purpose Echo planar time‐resolved imaging (EPTI) is a new imaging approach that addresses the limitations of EPI by providing high‐resolution, distortion‐ and T2/T2*$$ {\mathrm{T}}_2^{\ast } $$ blurring–free imaging for functional MRI (fMRI). However, as in all multishot sequences, intershot phase variations induced by physiological processes can i...
Article
Full-text available
Advances in the spatiotemporal resolution and field-of-view of neuroimaging tools are driving mesoscale studies for translational neuroscience. On October 10, 2023, the Center for Mesoscale Mapping (CMM) at the Massachusetts General Hospital (MGH) Athinoula A. Martinos Center for Biomedical Imaging and the Massachusetts Institute of Technology (MIT...
Article
Full-text available
Magnetic resonance angiography (MRA) performed at ultra-high magnetic field provides a unique opportunity to study the arteries of the living human brain at the mesoscopic level. From this, we can gain new insights into the brain's blood supply and vascular disease affecting small vessels. However, for quantitative characterization and precise repr...
Preprint
Full-text available
Magnetic resonance angiography (MRA) performed at ultra-high magnetic field provides a unique opportunity to study the arteries of the living human brain at the mesoscopic level. From this, we can gain new insights into the brain's blood supply and vascular disease affecting small vessels. However, for quantitative characterization and precise repr...
Article
Full-text available
United States (US) Special Operations Forces (SOF) are frequently exposed to explosive blasts in training and combat, but the effects of repeated blast exposure (RBE) on SOF brain health are incompletely understood. Furthermore, there is no diagnostic test to detect brain injury from RBE. As a result, SOF personnel may experience cognitive, physica...
Preprint
Full-text available
Macrovascular biases have been a long-standing challenge for fMRI, limiting its ability to detect spatially specific neural activity. Recent experimental studies, including our own (Huck et al., 2023; Zhong et al., 2023), found substantial resting-state macrovascular BOLD fMRI contributions from large veins and arteries, extending into the perivasc...
Preprint
Full-text available
The ability to detect fast responses with functional MRI depends on the speed of hemodynamic responses to neural activity, because hemodynamic responses act as a temporal low-pass filter smoothing out rapid changes. However, hemodynamic responses (their shape and timing) are highly variable across the brain and across stimuli. This heterogeneity of...
Article
Background: Previous case reports suggested co-localization of tau but not β-Amyloid with cortical superficial siderosis (cSS) in cerebral amyloid angiopathy (CAA). We thus hypothesized that the tau load represents a continuum with amyloid accumulation in the disease cascade and that the tau load would be higher in lobes with cSS and intracerebral...
Preprint
Full-text available
Purpose: To overcome the major challenges in diffusion MRI acquisition, including low SNR, distortion/blurring, and motion vulnerability. Methods: A novel Romer-EPTI technique is developed to provide high SNR, sharp spatial resolution, high motion-robustness, images free from distortion and slab-boundary artifacts, and simultaneous multi-TE imaging...
Preprint
Full-text available
Purpose: To develop EPTI, a multi-shot distortion-free multi-echo imaging technique, into a single-shot acquisition to achieve improved robustness to motion and physiological noise, increased temporal resolution, and high SNR efficiency for dynamic imaging applications. Methods: A new spatiotemporal encoding was developed to achieve single-shot EPT...
Preprint
Full-text available
Neuroimaging studies of the functional organization of human auditory cortex have focused on group-level analyses to identify tendencies that represent the typical brain. Here, we mapped auditory areas of the human superior temporal cortex (STC) in 30 participants by combining functional network analysis and 1-mm isotropic resolution 7T functional...
Preprint
Full-text available
In graph theory, "multilayer networks" represent systems involving several interconnected topological levels. A neuroscience example is the hierarchy of connections between different cortical depths or "lamina". This hierarchy is becoming non-invasively accessible in humans using ultra-high-resolution functional MRI (fMRI). Here, we applied multila...
Article
Full-text available
To increase granularity in human neuroimaging science, we designed and built a next-generation 7 Tesla magnetic resonance imaging scanner to reach ultra-high resolution by implementing several advances in hardware. To improve spatial encoding and increase the image signal-to-noise ratio, we developed a head-only asymmetric gradient coil (200 mT m⁻¹...
Article
Full-text available
United States Special Operations Forces (SOF) personnel are frequently exposed to explosive blasts in training and combat. However, the effects of repeated blast exposure on the human brain are incompletely understood. Moreover, there is currently no diagnostic test to detect repeated blast brain injury (rBBI). In this "Human Performance Optimizati...
Article
Speech and language processing involve complex interactions between cortical areas necessary for articulatory movements and auditory perception and a range of areas through which these are connected and interact. Despite their fundamental importance, the precise mechanisms underlying these processes are not fully elucidated. We measured BOLD signal...
Article
Full-text available
In this editorial we introduce a new non-profit open access journal, Imaging Neuroscience. In April 2023, editors of the journals NeuroImage and NeuroImage:Reports resigned, and a month later launched Imaging Neuroscience. NeuroImage had long been the leading journal in the field of neuroimaging. While the move to fully open access in 2020 represen...
Preprint
Full-text available
BACKGROUND: The association between brain regions involved in speech production and those that play a role in speech perception is not yet fully understood. We compared speech production related brain activity with activations resulting from perceptual categorization of syllables using high field 7 Tesla functional magnetic resonance imaging (fMRI)...
Article
Full-text available
Diffusion MRI is a useful neuroimaging tool for non-invasive mapping of human brain microstructure and structural connections. The analysis of diffusion MRI data often requires brain segmentation, including volumetric segmentation and cerebral cortical surfaces, from additional high-resolution T1-weighted (T1w) anatomical MRI data, which may be una...
Article
Full-text available
Background Cerebral Amyloid Angiopathy (CAA) is a cerebral small vessel disease that can lead to microstructural disruption of white matter (WM), which can be measured by the Peak Width of Skeletonized Mean Diffusivity (PSMD). We hypothesized that PSMD measures would be increased in patients with CAA compared to healthy controls (HC), and increased...
Article
Full-text available
The characterization of cortical myelination is essential for the study of structure-function relationships in the human brain. However, knowledge about cortical myelination is largely based on post-mortem histology, which generally renders direct comparison to function impossible. The repeating pattern of pale-thin-pale-thick stripes of cytochrome...
Article
Background and Purpose: We aimed to compare the amyloid load and degree of microstructural injury among Cerebral Amyloid Angiopathy (CAA) patients with either higher lobar cerebral microbleed (CMB) counts or higher cortical superficial siderosis (cSS) extent against CAA patients with lower hemorrhagic load. Methods: The study included 38 cognitivel...
Article
Full-text available
Purpose To achieve high‐resolution multishot echo‐planar imaging (EPI) for functional MRI (fMRI) with reduced sensitivity to in‐plane motion and between‐shot phase variations. Methods Two‐dimensional radiofrequency pulses were incorporated in a multishot EPI sequence at 7T which selectively excited a set of in‐plane bands (shutters) in the phase e...
Chapter
Brain motion interferes with functional magnetic resonance imaging (fMRI) by causing a variety of signal artifacts whose characteristics depend on the kind of motion, the pulse sequence used, and when and how the motion occurred. In task fMRI, motion artifact uncorrelated with the task design degrades statistical power by introducing noise, causing...
Preprint
Neural network (NN) based approaches for super-resolution MRI typically require high-SNR high-resolution reference data acquired in many subjects, which is time consuming and a barrier to feasible and accessible implementation. We propose to train NNs for Super-Resolution using Noisy Reference data (SRNR), leveraging the mechanism of the classic NN...
Article
T1 relaxation times of the 14 T1 phantom spheres that make up the standard ISMRM/NIST system phantom are being reported at 7 T. T1 values of six out of the 14 T1 spheres at 7 T (with T1 > 270 ms) have been reported previously but to the best of our knowledge, not all the T1s of the 14 T1 spheres at 7 T have been reported before. Given the increasin...
Article
Full-text available
Accurate spatial alignment of MRI data acquired across multiple contrasts in the same subject is often crucial for data analysis and interpretation, but can be challenging in the presence of geometric distortions that differ between acquisitions. It is well known that single-shot echo-planar imaging (EPI) acquisitions suffer from distortion in the...
Article
Full-text available
Awakening from sleep reflects a profound transformation in neural activity and behavior. The thalamus is a key controller of arousal state, but whether its diverse nuclei exhibit coordinated or distinct activity at transitions in behavioral arousal state is unknown. Using fast fMRI at ultra-high field (7 Tesla), we measured sub-second activity acro...
Article
Full-text available
Purpose To implement a method for real‐time field control using rapid FID navigator (FIDnav) measurements and evaluate the efficacy of the proposed approach for mitigating dynamic field perturbations and improving T2*$$ {\mathrm{T}}_2^{\ast } $$‐weighted image quality. Methods FIDnavs were embedded in a gradient echo sequence and a subject‐specifi...
Article
Full-text available
Invasive neurophysiological studies in nonhuman primates have shown different laminar activation profiles to auditory vs. visual stimuli in auditory cortices and adjacent polymodal areas. Means to examine the underlying feedforward vs. feedback type influences noninvasively have been limited in humans. Here, using 1‐mm isotropic resolution 3D echo‐...
Article
White matter lesions (WML) have been linked to cognitive decline in aging as well as in Alzheimer’s disease. While hypoperfusion is frequently considered a cause of WMLs due to the resulting reduction in oxygen availability to brain tissue, such reductions could also be caused by impaired oxygen exchange. Here, we tested the hypothesis that venous...
Article
Recent studies have reported functional MRI (fMRI) activation within cerebral white matter (WM) using blood-oxygenation-level-dependent (BOLD) contrast. Many blood vessels in WM run parallel to the fibre bundles, and other studies observed dependence of susceptibility contrast-based measures of blood volume on the local orientation of the fibre bun...
Article
Full-text available
Emerging evidence suggests that repeated blast exposure (RBE) is associated with brain injury in military personnel. United States (U.S.) Special Operations Forces (SOF) personnel experience high rates of blast exposure during training and combat, but the effects of low-level RBE on brain structure and function in SOF have not been comprehensively...
Article
Objective: Recent data suggest that cerebral amyloid angiopathy (CAA) causes haemorrhagic lesions in cerebellar cortex as well as subcortical cerebral atrophy. However, the potential effect of CAA on cerebellar tissue loss and its clinical implications have not been investigated. Methods: Our study included 70 non-demented patients with probable...
Article
Full-text available
The pial arterial vasculature of the human brain is the only blood supply to the neocortex, but quantitative data on the morphology and topology of these mesoscopic arteries (diameter 50-300µm) remains scarce. Because it is commonly assumed that blood flow velocities in these vessels are prohibitively slow, non-invasive time-of-flight MRI angiograp...
Preprint
Full-text available
The characterization of cortical myelination is essential for the study of structure-function relationships in the human brain. However, knowledge about cortical myelination is largely based on post mortem histology, which shows conflicting results depending on the staining method used, and generally renders direct comparison to function impossible...
Article
Full-text available
Ultra‐high Field (≥7T) functional magnetic resonance imaging (UHF‐fMRI) provides opportunities to resolve fine‐scale features of functional architecture such as cerebral cortical columns and layers, in vivo. While the nominal resolution of modern fMRI acquisitions may appear to be sufficient to resolve these features, several common data preprocess...
Article
Understanding how and why MR signals and their associated relaxation rates vary with cortical depth could ultimately enable the noninvasive investigation of the laminar architecture of cerebral cortex in the living human brain. However, cortical gray matter is typically only a few millimeters thick, making it challenging to sample many cortical dep...
Article
Full-text available
Diffusion tensor magnetic resonance imaging (DTI) is a widely adopted neuroimaging method for the in vivo mapping of brain tissue microstructure and white matter tracts. Nonetheless, the noise in the diffusion-weighted images (DWIs) decreases the accuracy and precision of DTI derived microstructural parameters and leads to prolonged acquisition tim...
Article
Background: Cerebral amyloid angiopathy (CAA) causes impaired vascular reactivity to physiologic stimuli that mediates CAA-related white matter hyperintensities (WMH) but its relationship to microstructural changes has not yet been tested. We hypothesized that the degree of vascular dysfunction would be associated with alterations in white matter m...
Article
We postulated that vascular dysfunction mediates the relationship between amyloid load and white matter hyperintensities (WMH) in cerebral amyloid angiopathy (CAA). Thirty-eight cognitively healthy patients with CAA (mean age 70 ± 7.1) were evaluated. WMH was quantified and expressed as percent of total intracranial volume (pWMH) using structural M...
Article
Full-text available
Strong gradient systems can improve the signal-to-noise ratio of diffusion MRI measurements and enable a wider range of acquisition parameters that are beneficial for microstructural imaging. We present a comprehensive diffusion MRI dataset of 26 healthy participants acquired on the MGH-USC 3 T Connectome scanner equipped with 300 mT/m maximum grad...
Preprint
Full-text available
Accurate spatial alignment of MRI data acquired across multiple contrasts in the same subject is often crucial for data analysis and interpretation, but can be challenging in the presence of geometric distortions that differ between acquisitions. It is well known that single-shot echo-planar imaging (EPI) acquisitions suffer from distortion in the...
Preprint
Full-text available
The moment of awakening from sleep reflects a profound transformation in neural activity and behavior. The thalamus is a key controller of arousal state, but whether its diverse nuclei exhibit coordinated or distinct activity at transitions in behavioral arousal state is not known. Using fast fMRI at ultra-high field (7 Tesla), we measured sub-seco...
Preprint
Full-text available
The noise in diffusion-weighted images (DWIs) decreases the accuracy and precision of diffusion tensor magnetic resonance imaging (DTI) derived microstructural parameters and leads to prolonged acquisition time for achieving improved signal-to-noise ratio (SNR). Deep learning-based image denoising using convolutional neural networks (CNNs) has supe...
Article
Full-text available
We tested how a stimulus gestalt, defined by the neuronal interaction between local and global features of a stimulus, is represented within human primary visual cortex (V1). We used high-resolution fMRI, which serves as a surrogate of neuronal activation, to measure co-fluctuations within subregions of V1 as (male and female) subjects were present...
Article
Full-text available
Purpose To test an integrated “AC/DC” array approach at 7T, where B0 inhomogeneity poses an obstacle for functional imaging, diffusion‐weighted MRI, MR spectroscopy, and other applications. Methods A close‐fitting 7T 31‐channel (31‐ch) brain array was constructed and tested using combined Rx and ΔB0 shim channels driven by a set of rapidly switcha...
Article
Full-text available
Spin-echo (SE) BOLD fMRI has high microvascular specificity, and thus provides a more reliable means to localize neural activity compared to conventional gradient-echo BOLD fMRI. However, the most common SE BOLD acquisition method, SE-EPI, is known to suffer from T2′ contrast contamination with undesirable draining vein bias. To address this, in th...
Article
Full-text available
Recent studies have demonstrated that fast fMRI can track neural activity well above the temporal limit predicted by the canonical hemodynamic response model. While these findings are promising, the biophysical mechanisms underlying these fast fMRI phenomena remain underexplored. In this study, we discuss two aspects of the hemodynamic response, co...
Presentation
Full-text available
The pial arterial vasculature of the human brain is the only blood supply to the neocortex, but quantitative data on the morphology and topology of these mesoscopic arteries (diameter 50–300 µm) remains scarce. Because it is commonly assumed that blood flow velocities in these vessels are prohibitively slow, non-invasive time-of-flight magnetic res...
Article
Fast fMRI enables the detection of neural dynamics over timescales of hundreds of milliseconds, suggesting it may provide a new avenue for studying subsecond neural processes in the human brain. The magnitudes of these fast fMRI dynamics are far greater than predicted by canonical models of the hemodynamic response. Several studies have established...
Article
Limited detection power has been a bottleneck for subject-specific functional MRI (fMRI) studies; however, the higher signal-to-noise ratio afforded by ultra-high magnetic fields (≥7 Tesla) provides levels of sensitivity and resolution needed to study individual subjects. What may be surprising is that higher imaging resolution may provide both hig...
Article
Full-text available
Background and purpose: Age-related macular degeneration is associated with reduced perfusion of the eye; however, the role of altered blood flow in the upstream ophthalmic or internal carotid arteries is unclear. We used ultra-high-field MR imaging to investigate whether the diameter of and blood flow in the ophthalmic artery and/or the ICA are a...
Preprint
Full-text available
The pial arterial vasculature of the human brain is the only blood supply to the neocortex, but quantitative data on the morphology and topology of these mesoscopic vessels (diameter 50-300 μm) remains scarce. Because it is commonly assumed that blood flow velocities in these vessels are prohibitively slow, non-invasive time-of-flight MRI angiograp...
Preprint
Full-text available
Spin-echo (SE) BOLD fMRI has high microvascular specificity, but its most common acquisition method, SE-EPI, suffers from T2' contrast contamination with undesirable draining vein bias. To address this, in this study, we extended a recently developed multi-shot EPI technique, Echo-Planar Time-resolved Imaging (EPTI), to laminar SE-fMRI at 7T to obt...
Article
Full-text available
We present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy participant. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-...
Article
Full-text available
Purpose Most voxels in white matter contain multiple fiber populations with different orientations and levels of myelination. Conventional T1 mapping measures 1 T1 value per voxel, representing a weighted average of the multiple tract T1 times. Inversion‐recovery diffusion‐weighted imaging (IR‐DWI) allows the T1 times of multiple tracts in a voxel...
Article
Background: We hypothesized that Peak Width of Skeletonized Mean Diffusivity (PSMD), an automated marker of cerebral microangiopathy representing microstructural disruption of white matter (WM), would be increased in patients with cerebral amyloid angiopathy (CAA) compared to healthy controls (HCs) and increased PSMD would be associated with lower...
Article
Background: Cerebral amyloid angiopathy (CAA) is associated with white matter hyperintensities (WMH) but the physiopathological mechanisms remain unclear. We hypothesized that the relationship between vascular amyloid load and WMH is mediated by vascular dysfunction. Methods: The study cohort included 38 non-demented probable CAA patients who under...
Article
Background: The mechanisms linking cerebral amyloid angiopathy (CAA) to enlarged perivascular spaces in centrum semiovale (CSO-EPVS) and whether other Alzheimer’s Disease (AD) pathologies might affect CSO-EPVS are unclear. We hypothesized that amyloid but not tau load would independently correlate with CSO-EPVS in CAA. Methods: Fifty prospectively...
Article
Full-text available
Automatic cerebral cortical surface reconstruction is a useful tool for cortical anatomy quantification, analysis and visualization. Recently, the Human Connectome Project and several studies have shown the advantages of using T1-weighted magnetic resonance (MR) images with sub-millimeter isotropic spatial resolution instead of the standard 1-milli...
Article
Background: Recent data show that cerebral amyloid angiopathy (CAA) might cause hemorrhagic lesions in cerebellar cortex as well as cerebral atrophy. However, the potential effect of CAA on cerebellar tissue loss and its clinical implications have not been investigated. Methods: We compared cerebellar volumes in 70 nondemented patients with probabl...
Preprint
Full-text available
High-resolution diffusion tensor imaging (DTI) is beneficial for probing tissue microstructure in fine neuroanatomical structures, but long scan times and limited signal-to-noise ratio pose significant barriers to acquiring DTI at sub-millimeter resolution. To address this challenge, we propose a deep learning-based super-resolution method entitled...
Article
Objective: We aimed to analyze the relationship of lacunes with cortical cerebral microinfarcts (CMI), to assess their association with vascular dysfunction and to evaluate their effect on the risk of incident intracerebral hemorrhage (ICH) in cerebral amyloid angiopathy (CAA). Methods: The count and topography of lacunes (deep/lobar), CMIs and...
Article
Recent developments in optical microscopy, applicable for large-scale and longitudinal imaging of cortical activity in behaving animals, open unprecedented opportunities to gain a deeper understanding of neurovascular and neurometabolic coupling during different brain states. Future studies will leverage these tools to deliver foundational knowledg...
Chapter
Functional MRI (fMRI) represents a key application of neuroimaging at ultra-high field strengths, because the dramatic increase in fMRI sensitivity with field strength enables new classes of experiments not possible at conventional field strengths. Recent insights indicate that, although fMRI tracks neural activity indirectly through measuring the...
Article
Identifying a structural brain lesion on MRI has important implications in epilepsy and is the most important correlate to seizure freedom after surgery in patients with drug-resistant focal onset epilepsy. However, at conventional magnetic field strengths (1.5 and 3T) only around 60-85% of MRI examinations reveal such lesions. Over the last decade...
Article
Full-text available
The fMRI community has made great strides in decoupling neuronal activity from other physiologically induced T2* changes, using sensors that provide a ground-truth with respect to cardiac, respiratory, and head movement dynamics. However, blood oxygenation level-dependent (BOLD) time-series dynamics are also confounded by scanner artifacts, in comp...
Preprint
Full-text available
We present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy subject. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-stre...
Article
Full-text available
Purpose To develop a method for slice‐wise dynamic distortion correction for EPI using rapid spatiotemporal B0 field measurements from FID navigators (FIDnavs) and to evaluate the efficacy of this new approach relative to an established data‐driven technique. Methods A low‐resolution reference image was used to create a forward model of FIDnav sig...
Preprint
Full-text available
Automatic cerebral cortical surface reconstruction is a useful tool for cortical anatomy quantification, analysis and visualization. Recently, the Human Connectome Project and several studies have shown the advantages of using T 1 -weighted magnetic resonance (MR) images with sub-millimeter isotropic spatial resolution instead of the standard 1-mil...
Article
Accurate and automated reconstruction of the in vivo human cerebral cortical surface from anatomical magnetic resonance (MR) images facilitates the quantitative analysis of cortical structure. Anatomical MR images with sub-millimeter isotropic spatial resolution improve the accuracy of cortical surface and thickness estimation compared to the stand...
Article
Full-text available
Purpose The goal of this study was to measure diffusion signals within the cerebral cortex using the line‐scan technique to achieve extremely high resolution in the radial direction (ie, perpendicular to the cortical surface) and to demonstrate the utility of these measurements for investigating laminar architecture in the living human brain. Meth...
Article
We demonstrate that non-rigid deformations of, e.g., the mouth introduce bias in the vNav-based detection of brain motion, which causes artifacts. We present real-time brain extraction for vNavs and show that these artifacts can be removed by brain-masked registration.
Article
Full-text available
Purpose To alleviate the spatial encoding limitations of single‐shot echo‐planar imaging (EPI) by developing multi‐shot segmented EPI for ultra‐high‐resolution functional MRI (fMRI) with reduced ghosting artifacts from subject motion and respiration. Theory and Methods Segmented EPI can reduce readout duration and reduce acceleration factors, howe...
Preprint
Purpose To alleviate the spatial encoding limitations of single-shot EPI by developing multi-shot segmented EPI for ultra-high-resolution fMRI with reduced ghosting artifacts from subject motion and respiration. Methods Segmented EPI can reduce readout duration and reduce acceleration factors, however, the time elapsed between segment acquisitions...
Article
Full-text available
Diffusion tensor magnetic resonance imaging (DTI) is unsurpassed in its ability to map tissue microstructure and structural connectivity in the living human brain. Nonetheless, the angular sampling requirement for DTI leads to long scan times and poses a critical barrier to performing high-quality DTI in routine clinical practice and large-scale re...
Article
Full-text available
The primary visual cortex of humans contains patches of neurons responding preferentially to stimulation of one eye (the ocular dominance columns). The majority of previous fMRI studies reporting eye-specific activity in V1 used magnetic field strengths of 4 T and higher. However, there have been reports of reliable eye-selective activations at 3 T...
Preprint
The fMRI community has made great strides in decoupling neuronal activity from other physiologically induced T2* changes, using sensors that provide a ground-truth with respect to cardiac, respiratory, and head movement dynamics. However, blood oxygenation level-dependent (BOLD) time-series dynamics are confounded by scanner artifacts, in complex w...
Article
Full-text available
Slow changes in systemic brain physiology can elicit large fluctuations in fMRI time series, which manifest as structured spatial patterns of temporal correlations between distant brain regions. Here, we investigated whether such "physiological networks"-sets of segregated brain regions that exhibit similar responses following slow changes in syste...
Article
Background: Cerebral Amyloid Angiopathy (CAA) emerged as an important contributor to cognitive impairment (CI) in elderly. Multiple lines of evidence suggest the presence of vascular dysfunction in CAA but its relationship to CI has not been tested. We hypothesized that the degree of vascular dysfunction identified by functional magnetic resonance...
Article
Introduction: Cerebral amyloid angiopathy (CAA) is an established cause of intracerebral hemorrhage and vascular dysfunction leading to ischemia. Functional connectivity analysis using MRI is becoming an important tool to analyze the brain activity during resting state, the default mode network (DMN) representing the prototypical set of connections...
Article
Full-text available
The temporal monocular crescent (TMC) is the most peripheral portion of the visual field whose perception relies solely on input from the ipsilateral eye. According to a handful of post-mortem histological studies in humans and non-human primates, the TMC is represented visuotopically within the most anterior portion of the primary visual cortical...
Article
Full-text available
Purpose Spin‐echo functional MRI (SE‐fMRI) has the potential to improve spatial specificity when compared with gradient‐echo fMRI. However, high spatiotemporal resolution SE‐fMRI with large slice‐coverage is challenging as SE‐fMRI requires a long echo time to generate blood oxygenation level‐dependent (BOLD) contrast, leading to long repetition tim...
Article
Full-text available
Functional imaging with sub-millimeter spatial resolution is a basic requirement for assessing functional MRI (fMRI) responses across different cortical depths, and is used extensively in the emerging field of laminar fMRI. Such studies seek to investigate the detailed functional organization of the brain and may develop to a new powerful tool for...

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