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Edward J. Auerbach

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YNIMG Journal 2025 Journal Article

Exploring in vivo human brain metabolism at 10.5 T: Initial insights from MR spectroscopic imaging

  • Lukas Hingerl
  • Bernhard Strasser
  • Simon Schmidt
  • Korbinian Eckstein
  • Guglielmo Genovese
  • Edward J. Auerbach
  • Andrea Grant
  • Matt Waks

INTRODUCTION: Ultra-high-field magnetic resonance (MR) systems (7 T and 9.4 T) offer the ability to probe human brain metabolism with enhanced precision. Here, we present the preliminary findings from 3D MR spectroscopic imaging (MRSI) of the human brain conducted with the world's first 10.5 T whole-body MR system. METHODS: -weighted MRI were obtained. RESULTS: = 65 ± 11° within the MRSI volume of interest. DISCUSSION: These preliminary findings highlight the potential of 10.5 T MRSI as a powerful imaging tool for probing cerebral metabolism. By providing unprecedented spatial and spectral resolution, this technology could offer a unique view into the metabolic intricacies of the human brain, but further technical developments will be necessary to optimize data quality and fully leverage the capabilities of 10.5 T MRSI.

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YNIMG Journal 2022 Journal Article

Empirical transmit field bias correction of T1w/T2w myelin maps

  • Matthew F. Glasser
  • Timothy S. Coalson
  • Michael P. Harms
  • Junqian Xu
  • Graham L. Baum
  • Joonas A. Autio
  • Edward J. Auerbach
  • Douglas N. Greve

T1-weighted divided by T2-weighted (T1w/T2w) myelin maps were initially developed for neuroanatomical analyses such as identifying cortical areas, but they are increasingly used in statistical comparisons across individuals and groups with other variables of interest. Existing T1w/T2w myelin maps contain radiofrequency transmit field (B1+) biases, which may be correlated with these variables of interest, leading to potentially spurious results. Here we propose two empirical methods for correcting these transmit field biases using either explicit measures of the transmit field or alternatively a 'pseudo-transmit' approach that is highly correlated with the transmit field at 3T. We find that the resulting corrected T1w/T2w myelin maps are both better neuroanatomical measures (e.g., for use in cross-species comparisons), and more appropriate for statistical comparisons of relative T1w/T2w differences across individuals and groups (e.g., sex, age, or body-mass-index) within a consistently acquired study at 3T. We recommend that investigators who use the T1w/T2w approach for mapping cortical myelin use these B1+ transmit field corrected myelin maps going forward.

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YNIMG Journal 2020 Journal Article

Ultra-high field (10.5 T) resting state fMRI in the macaque

  • Essa Yacoub
  • Mark D. Grier
  • Edward J. Auerbach
  • Russell L. Lagore
  • Noam Harel
  • Gregor Adriany
  • Anna Zilverstand
  • Benjamin Y. Hayden

Resting state functional connectivity refers to the temporal correlations between spontaneous hemodynamic signals obtained using functional magnetic resonance imaging. This technique has demonstrated that the structure and dynamics of identifiable networks are altered in psychiatric and neurological disease states. Thus, resting state network organizations can be used as a diagnostic, or prognostic recovery indicator. However, much about the physiological basis of this technique is unknown. Thus, providing a translational bridge to an optimal animal model, the macaque, in which invasive circuit manipulations are possible, is of utmost importance. Current approaches to resting state measurements in macaques face unique challenges associated with signal-to-noise, the need for contrast agents limiting translatability, and within-subject designs. These limitations can, in principle, be overcome through ultra-high magnetic fields. However, imaging at magnetic fields above 7T has yet to be adapted for fMRI in macaques. Here, we demonstrate that the combination of high channel count transmitter and receiver arrays, optimized pulse sequences, and careful anesthesia regimens, allows for detailed single-subject resting state analysis at high resolutions using a 10. 5 Tesla scanner. In this study, we uncover thirty spatially detailed resting state components that are highly robust across individual macaques and closely resemble the quality and findings of connectomes from large human datasets. This detailed map of the rsfMRI ‘macaque connectome’ will be the basis for future neurobiological circuit manipulation work, providing valuable biological insights into human connectomics.

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YNIMG Journal 2019 Journal Article

Human Connectome Project-style resting-state functional MRI at 7 Tesla using radiofrequency parallel transmission

  • Xiaoping Wu
  • Edward J. Auerbach
  • An T. Vu
  • Steen Moeller
  • Pierre-François Van de Moortele
  • Essa Yacoub
  • Kâmil Uğurbil

We investigate the utility of radiofrequency (RF) parallel transmission (pTx) for whole-brain resting-state functional MRI (rfMRI) acquisition at 7 Tesla (7T). To this end, Human Connectome Project (HCP)-style data acquisitions were chosen as a showcase example. Five healthy subjects were scanned in pTx and single-channel transmit (1Tx) modes. The pTx data were acquired using a prototype 16-channel transmit system and a commercially available Nova 8-channel transmit 32-channel receive RF head coil. Additionally, pTx single-spoke multiband (MB) pulses were designed to image sagittal slices. HCP-style 7T rfMRI data (1. 6-mm isotropic resolution, 5-fold slice and 2-fold in-plane acceleration, 3600 image volumes and ∼ 1-h scan) were acquired with pTx and the results were compared to those acquired with the original 7T HCP rfMRI protocol. The use of pTx significantly improved flip-angle uniformity across the brain, with coefficient of variation (i. e. , std/mean) of whole-brain flip-angle distribution reduced on average by ∼39%. This in turn yielded ∼17% increase in group temporal SNR (tSNR) as averaged across the entire brain and ∼10% increase in group functional contrast-to-noise ratio (fCNR) as averaged across the grayordinate space (including cortical surfaces and subcortical voxels). Furthermore, when placing a seed in either the posterior parietal lobe or putamen to estimate seed-based dense connectome, the increase in fCNR was observed to translate into stronger correlation of the seed with the rest of the grayordinate space. We have demonstrated the utility of pTx for slice-accelerated high-resolution whole-brain rfMRI at 7T; as compared to current state-of-the-art, the use of pTx improves flip-angle uniformity, increases tSNR, enhances fCNR and strengthens functional connectivity estimation.

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YNIMG Journal 2017 Journal Article

Tradeoffs in pushing the spatial resolution of fMRI for the 7T Human Connectome Project

  • An T. Vu
  • Keith Jamison
  • Matthew F. Glasser
  • Stephen M. Smith
  • Timothy Coalson
  • Steen Moeller
  • Edward J. Auerbach
  • Kamil Uğurbil

Whole-brain functional magnetic resonance imaging (fMRI), in conjunction with multiband acceleration, has played an important role in mapping the functional connectivity throughout the entire brain with both high temporal and spatial resolution. Ultrahigh magnetic field strengths (7T and above) allow functional imaging with even higher functional contrast-to-noise ratios for improved spatial resolution and specificity compared to traditional field strengths (1. 5T and 3T). High-resolution 7T fMRI, however, has primarily been constrained to smaller brain regions given the amount of time it takes to acquire the number of slices necessary for high resolution whole brain imaging. Here we evaluate a range of whole-brain high-resolution resting state fMRI protocols (0. 9, 1. 25, 1. 5, 1. 6 and 2mm isotropic voxels) at 7T, obtained with both in-plane and slice acceleration parallel imaging techniques to maintain the temporal resolution and brain coverage typically acquired at 3T. Using the processing pipeline developed by the Human Connectome Project, we demonstrate that high resolution images acquired at 7T provide increased functional contrast to noise ratios with significantly less partial volume effects and more distinct spatial features, potentially allowing for robust individual subject parcellations and descriptions of fine-scaled patterns, such as visuotopic organization.

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YNIMG Journal 2016 Journal Article

Evaluation of 2D multiband EPI imaging for high-resolution, whole-brain, task-based fMRI studies at 3T: Sensitivity and slice leakage artifacts

  • Nick Todd
  • Steen Moeller
  • Edward J. Auerbach
  • Essa Yacoub
  • Guillaume Flandin
  • Nikolaus Weiskopf

Functional magnetic resonance imaging (fMRI) studies that require high-resolution whole-brain coverage have long scan times that are primarily driven by the large number of thin slices acquired. Two-dimensional multiband echo-planar imaging (EPI) sequences accelerate the data acquisition along the slice direction and therefore represent an attractive approach to such studies by improving the temporal resolution without sacrificing spatial resolution. In this work, a 2D multiband EPI sequence was optimized for 1. 5mm isotropic whole-brain acquisitions at 3T with 10 healthy volunteers imaged while performing simultaneous visual and motor tasks. The performance of the sequence was evaluated in terms of BOLD sensitivity and false-positive activation at multiband (MB) factors of 1, 2, 4, and 6, combined with in-plane GRAPPA acceleration of 2× (GRAPPA 2), and the two reconstruction approaches of Slice-GRAPPA and Split Slice-GRAPPA. Sensitivity results demonstrate significant gains in temporal signal-to-noise ratio (tSNR) and t-score statistics for MB 2, 4, and 6 compared to MB 1. The MB factor for optimal sensitivity varied depending on anatomical location and reconstruction method. When using Slice-GRAPPA reconstruction, evidence of false-positive activation due to signal leakage between simultaneously excited slices was seen in one instance, 35 instances, and 70 instances over the ten volunteers for the respective accelerations of MB 2×GRAPPA 2, MB 4×GRAPPA 2, and MB 6×GRAPPA 2. The use of Split Slice-GRAPPA reconstruction suppressed the prevalence of false positives significantly, to 1 instance, 5 instances, and 5 instances for the same respective acceleration factors. Imaging protocols using an acceleration factor of MB 2×GRAPPA 2 can be confidently used for high-resolution whole-brain imaging to improve BOLD sensitivity with very low probability for false-positive activation due to slice leakage. Imaging protocols using higher acceleration factors (MB 3 or MB 4×GRAPPA 2) can likely provide even greater gains in sensitivity but should be carefully optimized to minimize the possibility of false activations.

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YNIMG Journal 2015 Journal Article

Theoretical and experimental evaluation of multi-band EPI for high-resolution whole brain pCASL Imaging

  • Xiufeng Li
  • Dingxin Wang
  • Edward J. Auerbach
  • Steen Moeller
  • Kamil Ugurbil
  • Gregory J. Metzger

Multi-band echo planar imaging (MB-EPI), a new approach to increase data acquisition efficiency and/or temporal resolution, has the potential to overcome critical limitations of standard acquisition strategies for obtaining high-resolution whole brain perfusion imaging using arterial spin labeling (ASL). However, the use of MB also introduces confounding effects, such as spatially varying amplified thermal noise and leakage contamination, which have not been evaluated to date as to their effect on cerebral blood flow (CBF) estimation. In this study, both the potential benefits and confounding effects of MB-EPI were systematically evaluated through both simulation and experimentally using a pseudo-continuous arterial spin labeling (pCASL) strategy. These studies revealed that the amplified noise, given by the geometry factor (g-factor), and the leakage contamination, assessed by the total leakage factor (TLF), have a minimal impact on CBF estimation. Furthermore, it is demonstrated that MB-EPI greatly benefits high-resolution whole brain pCASL studies in terms of improved spatial and temporal signal-to-noise ratio efficiencies, and increases compliance with the assumptions of the commonly used single blood compartment model, resulting in improved CBF estimates.

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YNIMG Journal 2014 Journal Article

ICA-based artefact removal and accelerated fMRI acquisition for improved resting state network imaging

  • Ludovica Griffanti
  • Gholamreza Salimi-Khorshidi
  • Christian F. Beckmann
  • Edward J. Auerbach
  • Gwenaëlle Douaud
  • Claire E. Sexton
  • Enikő Zsoldos
  • Klaus P. Ebmeier

The identification of resting state networks (RSNs) and the quantification of their functional connectivity in resting-state fMRI (rfMRI) are seriously hindered by the presence of artefacts, many of which overlap spatially or spectrally with RSNs. Moreover, recent developments in fMRI acquisition yield data with higher spatial and temporal resolutions, but may increase artefacts both spatially and/or temporally. Hence the correct identification and removal of non-neural fluctuations is crucial, especially in accelerated acquisitions. In this paper we investigate the effectiveness of three data-driven cleaning procedures, compare standard against higher (spatial and temporal) resolution accelerated fMRI acquisitions, and investigate the combined effect of different acquisitions and different cleanup approaches. We applied single-subject independent component analysis (ICA), followed by automatic component classification with FMRIB's ICA-based X-noiseifier (FIX) to identify artefactual components. We then compared two first-level (within-subject) cleaning approaches for removing those artefacts and motion-related fluctuations from the data. The effectiveness of the cleaning procedures was assessed using time series (amplitude and spectra), network matrix and spatial map analyses. For time series and network analyses we also tested the effect of a second-level cleaning (informed by group-level analysis). Comparing these approaches, the preferable balance between noise removal and signal loss was achieved by regressing out of the data the full space of motion-related fluctuations and only the unique variance of the artefactual ICA components. Using similar analyses, we also investigated the effects of different cleaning approaches on data from different acquisition sequences. With the optimal cleaning procedures, functional connectivity results from accelerated data were statistically comparable or significantly better than the standard (unaccelerated) acquisition, and, crucially, with higher spatial and temporal resolution. Moreover, we were able to perform higher dimensionality ICA decompositions with the accelerated data, which is very valuable for detailed network analyses.

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YNIMG Journal 2013 Journal Article

Advances in diffusion MRI acquisition and processing in the Human Connectome Project

  • Stamatios N. Sotiropoulos
  • Saad Jbabdi
  • Junqian Xu
  • Jesper L. Andersson
  • Steen Moeller
  • Edward J. Auerbach
  • Matthew F. Glasser
  • Moises Hernandez

The Human Connectome Project (HCP) is a collaborative 5-year effort to map human brain connections and their variability in healthy adults. A consortium of HCP investigators will study a population of 1200 healthy adults using multiple imaging modalities, along with extensive behavioral and genetic data. In this overview, we focus on diffusion MRI (dMRI) and the structural connectivity aspect of the project. We present recent advances in acquisition and processing that allow us to obtain very high-quality in-vivo MRI data, whilst enabling scanning of a very large number of subjects. These advances result from 2years of intensive efforts in optimising many aspects of data acquisition and processing during the piloting phase of the project. The data quality and methods described here are representative of the datasets and processing pipelines that will be made freely available to the community at quarterly intervals, beginning in 2013.

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YNIMG Journal 2013 Journal Article

Evaluation of slice accelerations using multiband echo planar imaging at 3T

  • Junqian Xu
  • Steen Moeller
  • Edward J. Auerbach
  • John Strupp
  • Stephen M. Smith
  • David A. Feinberg
  • Essa Yacoub
  • Kâmil Uğurbil

We evaluate residual aliasing among simultaneously excited and acquired slices in slice accelerated multiband (MB) echo planar imaging (EPI). No in-plane accelerations were used in order to maximize and evaluate achievable slice acceleration factors at 3T. We propose a novel leakage (L-) factor to quantify the effects of signal leakage between simultaneously acquired slices. With a standard 32-channel receiver coil at 3T, we demonstrate that slice acceleration factors of up to eight (MB=8) with blipped controlled aliasing in parallel imaging (CAIPI), in the absence of in-plane accelerations, can be used routinely with acceptable image quality and integrity for whole brain imaging. Spectral analyses of single-shot fMRI time series demonstrate that temporal fluctuations due to both neuronal and physiological sources were distinguishable and comparable up to slice-acceleration factors of nine (MB=9). The increased temporal efficiency could be employed to achieve, within a given acquisition period, higher spatial resolution, increased fMRI statistical power, multiple TEs, faster sampling of temporal events in a resting state fMRI time series, increased sampling of q-space in diffusion imaging, or more quiet time during a scan.

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YNICL Journal 2013 Journal Article

In vivo 1H magnetic resonance spectroscopy in young-adult daily marijuana users

  • Ryan L. Muetzel
  • Małgorzata Marjańska
  • Paul F. Collins
  • Mary P. Becker
  • Romain Valabrègue
  • Edward J. Auerbach
  • Kelvin O. Lim
  • Monica Luciana

To date, there has been little work describing the neurochemical profile of young, heavy marijuana users. In this study, we examined 27 young-adult marijuana users and 26 healthy controls using single-voxel magnetic resonance spectroscopy on a 3T scanner. The voxel was placed in the dorsal striatum, and estimated concentrations of glutamate+glutamine, myo-inositol, taurine+glucose, total choline and total N-acetylaspartate were examined between groups. There were no overall group effects, but two metabolites showed group by sex interactions. Lower levels of glutamate+glutamine (scaled to total creatine) were observed in female, but not male, marijuana users compared to controls. Higher levels of myo-inositol were observed in female users compared to female non-users and to males in both groups. Findings are discussed in relation to patterns of corticostriatal connectivity and function, in the context of marijuana abuse.

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YNIMG Journal 2013 Journal Article

Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

  • Kamil Uğurbil
  • Junqian Xu
  • Edward J. Auerbach
  • Steen Moeller
  • An T. Vu
  • Julio M. Duarte-Carvajalino
  • Christophe Lenglet
  • Xiaoping Wu

The Human Connectome Project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce ‘functional connectivity’; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3T, leading to whole brain coverage with 2mm isotropic resolution in 0. 7s for fMRI, and 1. 25mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total dMRI data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7T magnetic field are also presented, targeting higher spatial resolution, enhanced specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields, and reduced power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure.

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YNIMG Journal 2013 Journal Article

Resting-state fMRI in the Human Connectome Project

  • Stephen M. Smith
  • Christian F. Beckmann
  • Jesper Andersson
  • Edward J. Auerbach
  • Janine Bijsterbosch
  • Gwenaëlle Douaud
  • Eugene Duff
  • David A. Feinberg

Resting-state functional magnetic resonance imaging (rfMRI) allows one to study functional connectivity in the brain by acquiring fMRI data while subjects lie inactive in the MRI scanner, and taking advantage of the fact that functionally related brain regions spontaneously co-activate. rfMRI is one of the two primary data modalities being acquired for the Human Connectome Project (the other being diffusion MRI). A key objective is to generate a detailed in vivo mapping of functional connectivity in a large cohort of healthy adults (over 1000 subjects), and to make these datasets freely available for use by the neuroimaging community. In each subject we acquire a total of 1h of whole-brain rfMRI data at 3T, with a spatial resolution of 2×2×2mm and a temporal resolution of 0. 7s, capitalizing on recent developments in slice-accelerated echo-planar imaging. We will also scan a subset of the cohort at higher field strength and resolution. In this paper we outline the work behind, and rationale for, decisions taken regarding the rfMRI data acquisition protocol and pre-processing pipelines, and present some initial results showing data quality and example functional connectivity analyses.

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