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Bevington CW, Hanania JU, Ferraresso G, Cheng JCK, Pavel A, Su D, Stoessl AJ, Sossi V. Novel voxelwise residual analysis of [ 11C]raclopride PET data improves detection of low-amplitude dopamine release. J Cereb Blood Flow Metab 2024; 44:757-771. [PMID: 37974315 DOI: 10.1177/0271678x231214823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Existing methods for voxelwise transient dopamine (DA) release detection rely on explicit kinetic modeling of the [11C]raclopride PET time activity curve, which at the voxel level is typically confounded by noise, leading to poor performance for detection of low-amplitude DA release-induced signals. Here we present a novel data-driven, task-informed method-referred to as Residual Space Detection (RSD)-that transforms PET time activity curves to a residual space where DA release-induced perturbations can be isolated and processed. Using simulations, we demonstrate that this method significantly increases detection performance compared to existing kinetic model-based methods for low-magnitude DA release (simulated +100% peak increase in basal DA concentration). In addition, results from nine healthy controls injected with a single bolus of [11C]raclopride performing a finger tapping motor task are shown as proof-of-concept. The ability to detect relatively low magnitudes of dopamine release in the human brain using a single bolus injection, while achieving higher statistical power than previous methods, may additionally enable more complex analyses of neurotransmitter systems. Moreover, RSD is readily generalizable to multiple tasks performed during a single PET scan, further extending the capabilities of task-based single-bolus protocols.
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Affiliation(s)
- Connor Wj Bevington
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
| | - Jordan U Hanania
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
| | - Giovanni Ferraresso
- Department of Mechanical Engineering, University of British Columbia, Vancouver, Canada
| | - Ju-Chieh Kevin Cheng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
- Pacific Parkinson's Research Centre, University of British Columbia, Vancouver, Canada
| | - Alexandra Pavel
- Pacific Parkinson's Research Centre, University of British Columbia, Vancouver, Canada
| | - Dongning Su
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - A Jon Stoessl
- Pacific Parkinson's Research Centre, University of British Columbia, Vancouver, Canada
- Faculty of Medicine, Division of Neurology, University of British Columbia, Vancouver, Canada
| | - Vesna Sossi
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
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2
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Yun SD, Küppers F, Shah NJ. Submillimeter fMRI Acquisition Techniques for Detection of Laminar and Columnar Level Brain Activation. J Magn Reson Imaging 2024; 59:747-766. [PMID: 37589385 DOI: 10.1002/jmri.28911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Since the first demonstration in the early 1990s, functional MRI (fMRI) has emerged as one of the most powerful, noninvasive neuroimaging tools to probe brain functions. Subsequently, fMRI techniques have advanced remarkably, enabling the acquisition of functional signals with a submillimeter voxel size. This innovation has opened the possibility of investigating subcortical neural activities with respect to the cortical depths or cortical columns. For this purpose, numerous previous works have endeavored to design suitable functional contrast mechanisms and dedicated imaging techniques. Depending on the choice of the functional contrast, functional signals can be detected with high sensitivity or with improved spatial specificity to the actual activation site, and the pertaining issues have been discussed in a number of earlier works. This review paper primarily aims to provide an overview of the subcortical fMRI techniques that allow the acquisition of functional signals with a submillimeter resolution. Here, the advantages and disadvantages of the imaging techniques will be described and compared. We also summarize supplementary imaging techniques that assist in the analysis of the subcortical brain activation for more accurate mapping with reduced geometric deformation. This review suggests that there is no single universally accepted method as the gold standard for subcortical fMRI. Instead, the functional contrast and the corresponding readout imaging technique should be carefully determined depending on the purpose of the study. Due to the technical limitations of current fMRI techniques, most subcortical fMRI studies have only targeted partial brain regions. As a future prospect, the spatiotemporal resolution of fMRI will be pushed to satisfy the community's need for a deeper understanding of whole-brain functions and the underlying connectivity in order to achieve the ultimate goal of a time-resolved and layer-specific spatial scale. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 1.
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Affiliation(s)
- Seong Dae Yun
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
| | - Fabian Küppers
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
- RWTH Aachen University, Aachen, Germany
- Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany
- JARA - BRAIN - Translational Medicine, Aachen, Germany
- Department of Neurology, RWTH Aachen University, Aachen, Germany
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3
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Gomez DEP, Polimeni JR, Lewis LD. The temporal specificity of BOLD fMRI is systematically related to anatomical and vascular features of the human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578428. [PMID: 38352610 PMCID: PMC10862860 DOI: 10.1101/2024.02.01.578428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
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 responses implies that the temporal specificity of fMRI signals, or the ability of fMRI to preserve fast information, should also vary substantially across the cortex. In this work we investigated how local differences in hemodynamic response timing impact the temporal specificity of fMRI. We conducted our research using ultra-high field (7T) fMRI at high spatiotemporal resolution, using the primary visual cortex (V1) as a model area for investigation. We used visual stimuli oscillating at slow and fast frequencies to probe the temporal specificity of individual voxels. As expected, we identified substantial variability in temporal specificity, with some voxels preserving their responses to fast neural activity more effectively than others. We investigated which voxels had the highest temporal specificity and related those to anatomical and vascular features of V1. We found that low temporal specificity is only weakly explained by the presence of large veins or cerebral cortical depth. Notably, however, temporal specificity depended strongly on a voxel's position along the anterior-posterior anatomical axis of V1, with voxels within the calcarine sulcus being capable of preserving close to 25% of their amplitude as the frequency of stimulation increased from 0.05-Hz to 0.20-Hz, and voxels nearest to the occipital pole preserving less than 18%. These results indicate that detection biases in high-resolution fMRI will depend on the anatomical and vascular features of the area being imaged, and that these biases will differ depending on the timing of the underlying neuronal activity. Importantly, this spatial heterogeneity of temporal specificity suggests that it could be exploited to achieve higher specificity in some locations, and that tailored data analysis strategies may help improve the detection and interpretation of fast fMRI responses.
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Affiliation(s)
- Daniel E. P. Gomez
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
- Department of Radiology, Harvard Medical School, Boston, MA, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jonathan R. Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
- Department of Radiology, Harvard Medical School, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Laura D. Lewis
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, United States
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, United States
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4
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Heij J, Raimondo L, Siero JCW, Dumoulin SO, van der Zwaag W, Knapen T. A selection and targeting framework of cortical locations for line-scanning fMRI. Hum Brain Mapp 2023; 44:5471-5484. [PMID: 37608563 PMCID: PMC10543358 DOI: 10.1002/hbm.26459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/15/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Depth-resolved functional magnetic resonance imaging (fMRI) is an emerging field growing in popularity given the potential of separating signals from different computational processes in cerebral cortex. Conventional acquisition schemes suffer from low spatial and temporal resolutions. Line-scanning methods allow depth-resolved fMRI by sacrificing spatial coverage to sample blood oxygenated level-dependent (BOLD) responses at ultra-high temporal and spatial resolution. For neuroscience applications, it is critical to be able to place the line accurately to (1) sample the right neural population and (2) target that neural population with tailored stimuli or tasks. To this end, we devised a multi-session framework where a target cortical location is selected based on anatomical and functional properties. The line is then positioned according to this information in a separate second session, and we tailor the experiment to focus on the target location. Anatomically, the precision of the line placement was confirmed by projecting a nominal representation of the acquired line back onto the surface. Functional estimates of neural selectivities in the line, as quantified by a visual population-receptive field model, resembled the target selectivities well for most subjects. This functional precision was quantified in detail by estimating the distance between the visual field location of the targeted vertex and the location in visual cortex (V1) that most closely resembled the line-scanning estimates; this distance was on average ~5.5 mm. Given the dimensions of the line, differences in acquisition, session, and stimulus design, this validates that line-scanning can be used to probe local neural sensitivities across sessions. In summary, we present an accurate framework for line-scanning MRI; we believe such a framework is required to harness the full potential of line-scanning and maximize its utility. Furthermore, this approach bridges canonical fMRI experiments with electrophysiological experiments, which in turn allows novel avenues for studying human physiology non-invasively.
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Affiliation(s)
- Jurjen Heij
- Spinoza Centre for NeuroimagingAmsterdamNetherlands
- Department of Computational Cognitive Neuroscience and NeuroimagingNetherlands Institute for NeuroscienceAmsterdamNetherlands
- Department of Experimental and Applied PsychologyVU UniversityAmsterdamNetherlands
| | - Luisa Raimondo
- Spinoza Centre for NeuroimagingAmsterdamNetherlands
- Department of Computational Cognitive Neuroscience and NeuroimagingNetherlands Institute for NeuroscienceAmsterdamNetherlands
- Department of Experimental and Applied PsychologyVU UniversityAmsterdamNetherlands
| | - Jeroen C. W. Siero
- Spinoza Centre for NeuroimagingAmsterdamNetherlands
- Department of Computational Cognitive Neuroscience and NeuroimagingNetherlands Institute for NeuroscienceAmsterdamNetherlands
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Serge O. Dumoulin
- Spinoza Centre for NeuroimagingAmsterdamNetherlands
- Department of Computational Cognitive Neuroscience and NeuroimagingNetherlands Institute for NeuroscienceAmsterdamNetherlands
- Department of Experimental and Applied PsychologyVU UniversityAmsterdamNetherlands
- Department of Experimental PsychologyUtrecht UniversityUtrechtNetherlands
| | - Wietske van der Zwaag
- Spinoza Centre for NeuroimagingAmsterdamNetherlands
- Department of Computational Cognitive Neuroscience and NeuroimagingNetherlands Institute for NeuroscienceAmsterdamNetherlands
| | - Tomas Knapen
- Spinoza Centre for NeuroimagingAmsterdamNetherlands
- Department of Computational Cognitive Neuroscience and NeuroimagingNetherlands Institute for NeuroscienceAmsterdamNetherlands
- Department of Experimental and Applied PsychologyVU UniversityAmsterdamNetherlands
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Chang WT, Lin W, Giovanello KS. Enabling brain-wide mapping of directed functional connectivity at 3T via layer-dependent fMRI with draining-vein suppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563835. [PMID: 37961360 PMCID: PMC10634801 DOI: 10.1101/2023.10.24.563835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Layer-dependent functional magnetic resonance imaging (fMRI) offers a compelling avenue for investigating directed functional connectivity (FC). To construct a comprehensive map of brain-wide directed FC, several technical criteria must be met, including sub-mm spatial resolution, adequate temporal resolution, functional sensitivity, global brain coverage, and high spatial specificity. Although gradient echo (GE)-based echo planar imaging (EPI) is commonly used for rapid fMRI acquisition, it faces significant challenges due to the draining-vein effect, particularly when utilizing blood oxygen level-dependent (BOLD) contrast. In this study, we mitigated this effect by incorporating velocity-nulling (VN) gradients into a GE-BOLD fMRI sequence, opting for a 3T magnetic field strength over 7T. We also integrated several advanced techniques, such as simultaneous multi-slice (SMS) acceleration and NORDIC denoising, to enhance temporal resolution, spatial coverage, and signal sensitivity. Collectively, the VN fMRI method exhibited notable spatial specificity, as evidenced by the identification of double-peak activation patterns within the primary motor cortex (M1) during a finger-tapping task. Additionally, the technique demonstrated BOLD sensitivity in the lateral geniculate nucleus (LGN). Furthermore, our VN fMRI technique displayed superior robustness when compared to conventional fMRI approaches across participants. Our findings of directed FC elucidate several layer-specific functional relationships between different brain regions and align closely with existing literature. Given the widespread availability of 3T scanners, this technical advancement has the potential for significant impact across multiple domains of neuroscience research.
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Affiliation(s)
- Wei-Tang Chang
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, NC, USA
- Department of Radiology, University of North Carolina at Chapel Hill, NC, USA
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - Weili Lin
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, NC, USA
- Department of Radiology, University of North Carolina at Chapel Hill, NC, USA
| | - Kelly S. Giovanello
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, NC, USA
- Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill, NC, USA
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6
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Dresbach S, Huber LR, Gulban OF, Goebel R. Layer-fMRI VASO with short stimuli and event-related designs at 7 T. Neuroimage 2023; 279:120293. [PMID: 37562717 DOI: 10.1016/j.neuroimage.2023.120293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/06/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023] Open
Abstract
Layers and columns are the dominant processing units in the human (neo)cortex at the mesoscopic scale. While the blood oxygenation dependent (BOLD) signal has a high detection sensitivity, it is biased towards unwanted signals from large draining veins at the cortical surface. The additional fMRI contrast of vascular space occupancy (VASO) has the potential to augment the neuroscientific interpretability of layer-fMRI results by means of capturing complementary information of locally specific changes in cerebral blood volume (CBV). Specifically, VASO is not subject to unwanted sensitivity amplifications of large draining veins. Because of constrained sampling efficiency, it has been mainly applied in combination with efficient block task designs and long trial durations. However, to study cognitive processes in neuroscientific contexts, or probe vascular reactivity, short stimulation periods are often necessary. Here, we developed a VASO acquisition procedure with a short acquisition period and sub-millimeter resolution. During visual event-related stimulation, we show reliable responses in visual cortices within a reasonable number of trials (∼20). Furthermore, the short TR and high spatial specificity of our VASO implementation enabled us to show differences in laminar reactivity and onset times. Finally, we explore the generalizability to a different stimulus modality (somatosensation). With this, we showed that CBV-sensitive VASO provides the means to capture layer-specific haemodynamic responses with high spatio-temporal resolution and is able to be used with event-related paradigms.
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Affiliation(s)
- Sebastian Dresbach
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands.
| | - Laurentius Renzo Huber
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands; National Institute of Health, Bethesda, DC, USA
| | - Omer Faruk Gulban
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands; Brain Innovation, Maastricht, Netherlands
| | - Rainer Goebel
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands; Brain Innovation, Maastricht, Netherlands
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Uludağ K. Physiological modeling of the BOLD signal and implications for effective connectivity: A primer. Neuroimage 2023; 277:120249. [PMID: 37356779 DOI: 10.1016/j.neuroimage.2023.120249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023] Open
Abstract
In this primer, I provide an overview of the physiological processes that contribute to the observed BOLD signal (i.e., the generative biophysical model), including their time course properties within the framework of the physiologically-informed dynamic causal modeling (P-DCM). The BOLD signal is primarily determined by the change in paramagnetic deoxygenated hemoglobin, which results from combination of changes in oxygen metabolism, and cerebral blood flow and volume. Specifically, the physiological origin of the so-called BOLD signal "transients" will be discussed, including the initial overshoot, steady-state activation and the post-stimulus undershoot. I argue that incorrect physiological assumptions in the generative model of the BOLD signal can lead to incorrect inferences pertaining to both local neuronal activity and effective connectivity between brain regions. In addition, I introduce the recent laminar BOLD signal model, which extends P-DCM to cortical depths-resolved BOLD signals, allowing for laminar neuronal activity to be determined using high-resolution fMRI data.
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Affiliation(s)
- Kâmil Uludağ
- Krembil Brain Institute, University Health Network Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Center for Neuroscience Imaging Research, Institute for Basic Science & Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
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8
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Pais-Roldán P, Yun SD, Palomero-Gallagher N, Shah NJ. Cortical depth-dependent human fMRI of resting-state networks using EPIK. Front Neurosci 2023; 17:1151544. [PMID: 37274214 PMCID: PMC10232833 DOI: 10.3389/fnins.2023.1151544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/26/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Recent laminar-fMRI studies have substantially improved understanding of the evoked cortical responses in multiple sub-systems; in contrast, the laminar component of resting-state networks spread over the whole brain has been less studied due to technical limitations. Animal research strongly suggests that the supragranular layers of the cortex play a critical role in maintaining communication within the default mode network (DMN); however, whether this is true in this and other human cortical networks remains unclear. Methods Here, we used EPIK, which offers unprecedented coverage at sub-millimeter resolution, to investigate cortical broad resting-state dynamics with depth specificity in healthy volunteers. Results Our results suggest that human DMN connectivity is primarily supported by intermediate and superficial layers of the cortex, and furthermore, the preferred cortical depth used for communication can vary from one network to another. In addition, the laminar connectivity profile of some networks showed a tendency to change upon engagement in a motor task. In line with these connectivity changes, we observed that the amplitude of the low-frequency-fluctuations (ALFF), as well as the regional homogeneity (ReHo), exhibited a different laminar slope when subjects were either performing a task or were in a resting state (less variation among laminae, i.e., lower slope, during task performance compared to rest). Discussion The identification of varied laminar profiles concerning network connectivity, ALFF, and ReHo, observed across two brain states (task vs. rest) has major implications for the characterization of network-related diseases and suggests the potential diagnostic value of laminar fMRI in psychiatric disorders, e.g., to differentiate the cortical dynamics associated with disease stages linked, or not linked, to behavioral changes. The evaluation of laminar-fMRI across the brain encompasses computational challenges; nonetheless, it enables the investigation of a new dimension of the human neocortex, which may be key to understanding neurological disorders from a novel perspective.
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Affiliation(s)
- Patricia Pais-Roldán
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Seong Dae Yun
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Nicola Palomero-Gallagher
- Institute of Neuroscience and Medicine 1, Structural and Functional Organisation of the Brain, Forschungszentrum Jülich, Jülich, Germany
- C. and O. Vogt Institute for Brain Research, Heinrich-Heine-University, Düsseldorf, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen, Aachen, Germany
| | - N. Jon Shah
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11, Molecular Neuroscience and Neuroimaging, JARA, Forschungszentrum Jülich, Jülich, Germany
- JARA–BRAIN–Translational Medicine, Aachen, Germany
- Department of Neurology, RWTH Aachen University, Aachen, Germany
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9
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Ivanov D, De Martino F, Formisano E, Fritz FJ, Goebel R, Huber L, Kashyap S, Kemper VG, Kurban D, Roebroeck A, Sengupta S, Sorger B, Tse DHY, Uludağ K, Wiggins CJ, Poser BA. Magnetic resonance imaging at 9.4 T: the Maastricht journey. MAGMA (NEW YORK, N.Y.) 2023; 36:159-173. [PMID: 37081247 PMCID: PMC10140139 DOI: 10.1007/s10334-023-01080-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/22/2023]
Abstract
The 9.4 T scanner in Maastricht is a whole-body magnet with head gradients and parallel RF transmit capability. At the time of the design, it was conceptualized to be one of the best fMRI scanners in the world, but it has also been used for anatomical and diffusion imaging. 9.4 T offers increases in sensitivity and contrast, but the technical ultra-high field (UHF) challenges, such as field inhomogeneities and constraints set by RF power deposition, are exacerbated compared to 7 T. This article reviews some of the 9.4 T work done in Maastricht. Functional imaging experiments included blood oxygenation level-dependent (BOLD) and blood-volume weighted (VASO) fMRI using different readouts. BOLD benefits from shorter T2* at 9.4 T while VASO from longer T1. We show examples of both ex vivo and in vivo anatomical imaging. For many applications, pTx and optimized coils are essential to harness the full potential of 9.4 T. Our experience shows that, while considerable effort was required compared to our 7 T scanner, we could obtain high-quality anatomical and functional data, which illustrates the potential of MR acquisitions at even higher field strengths. The practical challenges of working with a relatively unique system are also discussed.
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Affiliation(s)
- Dimo Ivanov
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands.
| | - Federico De Martino
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Elia Formisano
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Francisco J Fritz
- Institute of Systems Neuroscience, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Rainer Goebel
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Laurentius Huber
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Sriranga Kashyap
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
| | - Valentin G Kemper
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Denizhan Kurban
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Alard Roebroeck
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | | | - Bettina Sorger
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
| | - Desmond H Y Tse
- Scannexus BV, Oxfordlaan 55, 6229 EV, Maastricht, The Netherlands
| | - Kâmil Uludağ
- Krembil Brain Institute, Koerner Scientist in MR Imaging, University Health Network Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Center for Neuroscience Imaging Research, Institute for Basic Science and Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Christopher J Wiggins
- Imaging Core Facility (INM-ICF), Institut für Neurowissenschaften und Medizin, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Benedikt A Poser
- Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
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Knudsen L, Bailey CJ, Blicher JU, Yang Y, Zhang P, Lund TE. Improved sensitivity and microvascular weighting of 3T laminar fMRI with GE-BOLD using NORDIC and phase regression. Neuroimage 2023; 271:120011. [PMID: 36914107 DOI: 10.1016/j.neuroimage.2023.120011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
INTRODUCTION Functional MRI with spatial resolution in the submillimeter domain enables measurements of activation across cortical layers in humans. This is valuable as different types of cortical computations, e.g., feedforward versus feedback related activity, take place in different cortical layers. Laminar fMRI studies have almost exclusively employed 7T scanners to overcome the reduced signal stability associated with small voxels. However, such systems are relatively rare and only a subset of those are clinically approved. In the present study, we examined if the feasibility of laminar fMRI at 3T could be improved by use of NORDIC denoising and phase regression. METHODS 5 healthy subjects were scanned on a Siemens MAGNETOM Prisma 3T scanner. To assess across-session reliability, each subject was scanned in 3-8 sessions on 3-4 consecutive days. A 3D gradient echo EPI (GE-EPI) sequence was used for BOLD acquisitions (voxel size 0.82 mm isotopic, TR = 2.2 s) using a block design finger tapping paradigm. NORDIC denoising was applied to the magnitude and phase time series to overcome limitations in temporal signal-to-noise ratio (tSNR) and the denoised phase time series were subsequently used to correct for large vein contamination through phase regression. RESULTS AND CONCLUSION NORDIC denoising resulted in tSNR values comparable to or higher than commonly observed at 7T. Layer-dependent activation profiles could thus be extracted robustly, within and across sessions, from regions of interest located in the hand knob of the primary motor cortex (M1). Phase regression led to substantially reduced superficial bias in obtained layer profiles, although residual macrovascular contribution remained. We believe the present results support an improved feasibility of laminar fMRI at 3T.
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Affiliation(s)
- Lasse Knudsen
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China.
| | - Christopher J Bailey
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China
| | - Jakob U Blicher
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark; Department of Neurology, Aalborg University Hospital, Aalborg, Denmark
| | - Yan Yang
- Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China; Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China
| | - Peng Zhang
- Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China; Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China
| | - Torben E Lund
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark
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11
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Dixon B, Sharkey JM, Teo EJ, Grace SA, Savage JS, Udy A, Smith P, Hellerstedt J, Santamaria JD. Assessment of a Non-Invasive Brain Pulse Monitor to Measure Intra-Cranial Pressure Following Acute Brain Injury. MEDICAL DEVICES (AUCKLAND, N.Z.) 2023; 16:15-26. [PMID: 36718229 PMCID: PMC9883992 DOI: 10.2147/mder.s398193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Background Intracranial pressure (ICP) monitoring requires placing a hole in the skull through which an invasive pressure monitor is inserted into the brain. This approach has risks for the patient and is expensive. We have developed a non-invasive brain pulse monitor that uses red light to detect a photoplethysmographic (PPG) signal arising from the blood vessels on the brain's cortical surface. The brain PPG and the invasive ICP waveform share morphological features which may allow measurement of the intracranial pressure. Methods We enrolled critically ill patients with an acute brain injury with invasive ICP monitoring to assess the new monitor. A total of 24 simultaneous invasive ICP and brain pulse monitor PPG measurements were undertaken in 12 patients over a range of ICP levels. Results The waveform morphologies were similar for the invasive ICP and brain pulse monitor PPG approach. Both methods demonstrated a progressive increase in the amplitude of P2 relative to P1 with increasing ICP levels. An automated algorithm was developed to assess the PPG morphological features in relation to the ICP level. A correlation was demonstrated between the brain pulse waveform morphology and ICP levels, R2=0.66, P < 0.001. Conclusion The brain pulse monitor's PPG waveform demonstrated morphological features were similar to the invasive ICP waveform over a range of ICP levels, these features may provide a method to measure ICP levels. Trial Registration ACTRN12620000828921.
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Affiliation(s)
- Barry Dixon
- Cyban Pty Ltd, Melbourne, VIC, Australia,Department of Critical Care Medicine, St Vincent’s Hospital, Melbourne, Australia,Department of Medicine, University of Melbourne, Melbourne, Vic, Australia,Correspondence: Barry Dixon, Department of Critical Care Medicine, St Vincent’s Hospital (Melbourne), 41 Victoria Parade, Fitzroy, VIC, 3065, Australia, Tel +61 3 9231 4425, Email
| | | | - Elliot J Teo
- Cyban Pty Ltd, Melbourne, VIC, Australia,Department of Critical Care Medicine, St Vincent’s Hospital, Melbourne, Australia
| | | | | | - Andrew Udy
- Department of Critical Care Medicine, The Alfred Hospital, Melbourne, Australia
| | - Paul Smith
- Department of Neurosurgery, St Vincent’s Hospital, Melbourne, Australia,University of Melbourne Medical School, Melbourne, Vic, Australia
| | | | - John D Santamaria
- Department of Critical Care Medicine, St Vincent’s Hospital, Melbourne, Australia
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12
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Improved laminar specificity and sensitivity by combining SE and GE BOLD signals. Neuroimage 2022; 264:119675. [PMID: 36243267 DOI: 10.1016/j.neuroimage.2022.119675] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/20/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The most widely used gradient-echo (GE) blood oxygenation level-dependent (BOLD) contrast has high sensitivity, but low specificity due to draining vein contributions, while spin-echo (SE) BOLD approach at ultra-high magnetic fields is highly specific to neural active sites but has lower sensitivity. To obtain high specificity and sensitivity, we propose to utilize a vessel-size-sensitive filter to the GE-BOLD signal, which suppresses macrovascular contributions and to combine selectively retained microvascular GE-BOLD signals with the SE-BOLD signals. To investigate our proposed idea, fMRI with 0.8 mm isotropic resolution was performed on the primary motor and sensory cortices in humans at 7 T by implementing spin- and gradient-echo (SAGE) echo planar imaging (EPI) acquisition. Microvascular-passed sigmoidal filters were designed based upon the vessel-size-sensitive ΔR2*/ΔR2 value for retaining GE-BOLD signals originating from venous vessels with ≤ 45 μm and ≤ 65 μm diameter. Unlike GE-BOLD fMRI, the laminar profile of SAGE-BOLD fMRI with the vessel-size-sensitive filter peaked at ∼ 1.0 mm from the surface of the primary motor and sensory cortices, demonstrating an improvement of laminar specificity over GE-BOLD fMRI. Also, the functional sensitivity of SAGE BOLD at middle layers (0.75-1.5 mm) was improved by ∼ 80% to ∼100% when compared with SE BOLD. In summary, we showed that combined GE- and SE-BOLD fMRI with the vessel-size-sensitive filter indeed yielded improved laminar specificity and sensitivity and is therefore an excellent tool for high spatial resolution ultra-high filed (UHF)-fMRI studies for resolving mesoscopic functional units.
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13
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Mesoscopic in vivo human T 2* dataset acquired using quantitative MRI at 7 Tesla. Neuroimage 2022; 264:119733. [PMID: 36375782 DOI: 10.1016/j.neuroimage.2022.119733] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/15/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
Mesoscopic (0.1-0.5 mm) interrogation of the living human brain is critical for advancing neuroscience and bridging the resolution gap with animal models. Despite the variety of MRI contrasts measured in recent years at the mesoscopic scale, in vivo quantitative imaging of T2* has not been performed. Here we provide a dataset containing empirical T2* measurements acquired at 0.35 × 0.35 × 0.35 mm3 voxel resolution using 7 Tesla MRI. To demonstrate unique features and high quality of this dataset, we generate flat map visualizations that reveal fine-scale cortical substructures such as layers and vessels, and we report quantitative depth-dependent T2* (as well as R2*) values in primary visual cortex and auditory cortex that are highly consistent across subjects. This dataset is freely available at https://doi.org/10.17605/OSF.IO/N5BJ7, and may prove useful for anatomical investigations of the human brain, as well as for improving our understanding of the basis of the T2*-weighted (f)MRI signal.
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14
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Demirayak P, Deshpande G, Visscher K. Laminar functional magnetic resonance imaging in vision research. Front Neurosci 2022; 16:910443. [PMID: 36267240 PMCID: PMC9577024 DOI: 10.3389/fnins.2022.910443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Magnetic resonance imaging (MRI) scanners at ultra-high magnetic fields have become available to use in humans, thus enabling researchers to investigate the human brain in detail. By increasing the spatial resolution, ultra-high field MR allows both structural and functional characterization of cortical layers. Techniques that can differentiate cortical layers, such as histological studies and electrode-based measurements have made critical contributions to the understanding of brain function, but these techniques are invasive and thus mainly available in animal models. There are likely to be differences in the organization of circuits between humans and even our closest evolutionary neighbors. Thus research on the human brain is essential. Ultra-high field MRI can observe differences between cortical layers, but is non-invasive and can be used in humans. Extensive previous literature has shown that neuronal connections between brain areas that transmit feedback and feedforward information terminate in different layers of the cortex. Layer-specific functional MRI (fMRI) allows the identification of layer-specific hemodynamic responses, distinguishing feedback and feedforward pathways. This capability has been particularly important for understanding visual processing, as it has allowed researchers to test hypotheses concerning feedback and feedforward information in visual cortical areas. In this review, we provide a general overview of successful ultra-high field MRI applications in vision research as examples of future research.
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Affiliation(s)
- Pinar Demirayak
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Pinar Demirayak,
| | - Gopikrishna Deshpande
- Department of Electrical and Computer Engineering, AU MRI Research Center, Auburn University, Auburn, AL, United States
- Department of Psychological Sciences, Auburn University, Auburn, AL, United States
- Alabama Advanced Imaging Consortium, Birmingham, AL, United States
- Center for Neuroscience, Auburn University, Auburn, AL, United States
- School of Psychology, Capital Normal University, Beijing, China
- Key Laboratory of Learning and Cognition, Capital Normal University, Beijing, China
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
- Centre for Brain Research, Indian Institute of Science, Bangalore, India
| | - Kristina Visscher
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
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15
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Akbari A, Bollmann S, Ali TS, Barth M. Modelling the depth-dependent VASO and BOLD responses in human primary visual cortex. Hum Brain Mapp 2022; 44:710-726. [PMID: 36189837 PMCID: PMC9842911 DOI: 10.1002/hbm.26094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 01/25/2023] Open
Abstract
Functional magnetic resonance imaging (fMRI) using a blood-oxygenation-level-dependent (BOLD) contrast is a common method for studying human brain function noninvasively. Gradient-echo (GRE) BOLD is highly sensitive to the blood oxygenation change in blood vessels; however, the spatial signal specificity can be degraded due to signal leakage from activated lower layers to superficial layers in depth-dependent (also called laminar or layer-specific) fMRI. Alternatively, physiological variables such as cerebral blood volume using the VAscular-Space-Occupancy (VASO) contrast have shown higher spatial specificity compared to BOLD. To better understand the physiological mechanisms such as blood volume and oxygenation changes and to interpret the measured depth-dependent responses, models are needed which reflect vascular properties at this scale. For this purpose, we extended and modified the "cortical vascular model" previously developed to predict layer-specific BOLD signal changes in human primary visual cortex to also predict a layer-specific VASO response. To evaluate the model, we compared the predictions with experimental results of simultaneous VASO and BOLD measurements in a group of healthy participants. Fitting the model to our experimental data provided an estimate of CBV change in different vascular compartments upon neural activity. We found that stimulus-evoked CBV change mainly occurs in small arterioles, capillaries, and intracortical arteries and that the contribution from venules and ICVs is smaller. Our results confirm that VASO is less susceptible to large vessel effects compared to BOLD, as blood volume changes in intracortical arteries did not substantially affect the resulting depth-dependent VASO profiles, whereas depth-dependent BOLD profiles showed a bias towards signal contributions from intracortical veins.
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Affiliation(s)
- Atena Akbari
- Centre for Advanced ImagingUniversity of QueenslandBrisbaneAustralia
| | - Saskia Bollmann
- Centre for Advanced ImagingUniversity of QueenslandBrisbaneAustralia
| | - Tonima S. Ali
- Centre for Advanced ImagingUniversity of QueenslandBrisbaneAustralia
| | - Markus Barth
- Centre for Advanced ImagingUniversity of QueenslandBrisbaneAustralia,ARC Training Centre for Innovation in Biomedical Imaging TechnologyThe University of QueenslandBrisbaneAustralia,School of Information Technology and Electrical EngineeringThe University of QueenslandBrisbaneQueenslandAustralia
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16
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John YJ, Sawyer KS, Srinivasan K, Müller EJ, Munn BR, Shine JM. It's about time: Linking dynamical systems with human neuroimaging to understand the brain. Netw Neurosci 2022; 6:960-979. [PMID: 36875012 PMCID: PMC9976648 DOI: 10.1162/netn_a_00230] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/04/2022] [Indexed: 11/04/2022] Open
Abstract
Most human neuroscience research to date has focused on statistical approaches that describe stationary patterns of localized neural activity or blood flow. While these patterns are often interpreted in light of dynamic, information-processing concepts, the static, local, and inferential nature of the statistical approach makes it challenging to directly link neuroimaging results to plausible underlying neural mechanisms. Here, we argue that dynamical systems theory provides the crucial mechanistic framework for characterizing both the brain's time-varying quality and its partial stability in the face of perturbations, and hence, that this perspective can have a profound impact on the interpretation of human neuroimaging results and their relationship with behavior. After briefly reviewing some key terminology, we identify three key ways in which neuroimaging analyses can embrace a dynamical systems perspective: by shifting from a local to a more global perspective, by focusing on dynamics instead of static snapshots of neural activity, and by embracing modeling approaches that map neural dynamics using "forward" models. Through this approach, we envisage ample opportunities for neuroimaging researchers to enrich their understanding of the dynamic neural mechanisms that support a wide array of brain functions, both in health and in the setting of psychopathology.
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Affiliation(s)
- Yohan J. John
- Neural Systems Laboratory, Department of Health Sciences, Boston University, Boston, MA, USA
| | - Kayle S. Sawyer
- Departments of Anatomy and Neurobiology, Boston University, Boston University, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Boston VA Healthcare System, Boston, MA, USA
- Sawyer Scientific, LLC, Boston, MA, USA
| | - Karthik Srinivasan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eli J. Müller
- Brain and Mind Center, University of Sydney, Sydney, NSW, Australia
| | - Brandon R. Munn
- Brain and Mind Center, University of Sydney, Sydney, NSW, Australia
| | - James M. Shine
- Brain and Mind Center, University of Sydney, Sydney, NSW, Australia
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17
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Chan RW, Cron GO, Asaad M, Edelman BJ, Lee HJ, Adesnik H, Feinberg D, Lee JH. Distinct local and brain-wide networks are activated by optogenetic stimulation of neurons specific to each layer of motor cortex. Neuroimage 2022; 263:119640. [PMID: 36176220 PMCID: PMC10025169 DOI: 10.1016/j.neuroimage.2022.119640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
Primary motor cortex (M1) consists of a stack of interconnected but distinct layers (L1-L6) which affect motor control through large-scale networks. However, the brain-wide functional influence of each layer is poorly understood. We sought to expand our knowledge of these layers' circuitry by combining Cre-driver mouse lines, optogenetics, fMRI, and electrophysiology. Neuronal activities initiated in Drd3 neurons (within L2/3) were mainly confined within M1, while stimulation of Scnn1a, Rbp4, and Ntsr1 neurons (within L4, L5, and L6, respectively) evoked distinct responses in M1 and motor-related subcortical regions, including striatum and motor thalamus. We also found that fMRI responses from targeted stimulations correlated with both local field potentials (LFPs) and spike changes. This study represents a step forward in our understanding of how different layers of primary motor cortex are embedded in brain-wide circuitry.
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Affiliation(s)
- Russell W Chan
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA
| | - Greg O Cron
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA
| | - Mazen Asaad
- Department of Molecular and Cellular Physiology, Stanford University, CA 94305, USA
| | - Bradley J Edelman
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA
| | - Hyun Joo Lee
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA
| | - Hillel Adesnik
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
| | - David Feinberg
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
| | - Jin Hyung Lee
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA; Department of Bioengineering, Stanford University, CA 94305, USA; Department of Neurosurgery, Stanford University, CA 94305, USA; Department of Electrical Engineering, Stanford University, CA 94305, USA.
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18
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Himmelberg MM, Gardner JL, Winawer J. What has vision science taught us about functional MRI? Neuroimage 2022; 261:119536. [PMID: 35931310 DOI: 10.1016/j.neuroimage.2022.119536] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 10/31/2022] Open
Abstract
In the domain of human neuroimaging, much attention has been paid to the question of whether and how the development of functional magnetic resonance imaging (fMRI) has advanced our scientific knowledge of the human brain. However, the opposite question is also important; how has our knowledge of the visual system advanced our understanding of fMRI? Here, we discuss how and why scientific knowledge about the human and animal visual system has been used to answer fundamental questions about fMRI as a brain measurement tool and how these answers have contributed to scientific discoveries beyond vision science.
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Affiliation(s)
- Marc M Himmelberg
- Department of Psychology, New York University, NY, USA; Center for Neural Science, New York University, NY, USA.
| | | | - Jonathan Winawer
- Department of Psychology, New York University, NY, USA; Center for Neural Science, New York University, NY, USA
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19
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Okada T, Fujimoto K, Fushimi Y, Akasaka T, Thuy DHD, Shima A, Sawamoto N, Oishi N, Zhang Z, Funaki T, Nakamoto Y, Murai T, Miyamoto S, Takahashi R, Isa T. Neuroimaging at 7 Tesla: a pictorial narrative review. Quant Imaging Med Surg 2022; 12:3406-3435. [PMID: 35655840 PMCID: PMC9131333 DOI: 10.21037/qims-21-969] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/05/2022] [Indexed: 01/26/2024]
Abstract
Neuroimaging using the 7-Tesla (7T) human magnetic resonance (MR) system is rapidly gaining popularity after being approved for clinical use in the European Union and the USA. This trend is the same for functional MR imaging (MRI). The primary advantages of 7T over lower magnetic fields are its higher signal-to-noise and contrast-to-noise ratios, which provide high-resolution acquisitions and better contrast, making it easier to detect lesions and structural changes in brain disorders. Another advantage is the capability to measure a greater number of neurochemicals by virtue of the increased spectral resolution. Many structural and functional studies using 7T have been conducted to visualize details in the white matter and layers of the cortex and hippocampus, the subnucleus or regions of the putamen, the globus pallidus, thalamus and substantia nigra, and in small structures, such as the subthalamic nucleus, habenula, perforating arteries, and the perivascular space, that are difficult to observe at lower magnetic field strengths. The target disorders for 7T neuroimaging range from tumoral diseases to vascular, neurodegenerative, and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy, major depressive disorder, and schizophrenia. MR spectroscopy has also been used for research because of its increased chemical shift that separates overlapping peaks and resolves neurochemicals more effectively at 7T than a lower magnetic field. This paper presents a narrative review of these topics and an illustrative presentation of images obtained at 7T. We expect 7T neuroimaging to provide a new imaging biomarker of various brain disorders.
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Affiliation(s)
- Tomohisa Okada
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Fujimoto
- Department of Real World Data Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasutaka Fushimi
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thai Akasaka
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Dinh H. D. Thuy
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Shima
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobukatsu Sawamoto
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoya Oishi
- Medial Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Zhilin Zhang
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Funaki
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuji Nakamoto
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Susumu Miyamoto
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Isa
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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20
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Pais-Roldán P, Yun SD, Shah NJ. Pre-processing of Sub-millimeter GE-BOLD fMRI Data for Laminar Applications. FRONTIERS IN NEUROIMAGING 2022; 1:869454. [PMID: 37555171 PMCID: PMC10406219 DOI: 10.3389/fnimg.2022.869454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/31/2022] [Indexed: 08/10/2023]
Abstract
Over the past 30 years, brain function has primarily been evaluated non-invasively using functional magnetic resonance imaging (fMRI) with gradient-echo (GE) sequences to measure blood-oxygen-level-dependent (BOLD) signals. Despite the multiple advantages of GE sequences, e.g., higher signal-to-noise ratio, faster acquisitions, etc., their relatively inferior spatial localization compromises the routine use of GE-BOLD in laminar applications. Here, in an attempt to rescue the benefits of GE sequences, we evaluated the effect of existing pre-processing methods on the spatial localization of signals obtained with EPIK, a GE sequence that affords voxel volumes of 0.25 mm3 with near whole-brain coverage. The methods assessed here apply to both task and resting-state fMRI data assuming the availability of reconstructed magnitude and phase images.
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Affiliation(s)
- Patricia Pais-Roldán
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Seong Dae Yun
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - N. Jon Shah
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11, Molecular Neuroscience and Neuroimaging, Jülich Aachen Research Alliance, Forschungszentrum Jülich, Jülich, Germany
- Jlich Aachen Research Alliance, Brain - Translational Medicine, Aachen, Germany
- Department of Neurology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
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21
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Cho S, Roy A, Liu CJ, Idiyatullin D, Zhu W, Zhang Y, Zhu XH, O'Herron P, Leikvoll A, Chen W, Kara P, Uğurbil K. Cortical layer-specific differences in stimulus selectivity revealed with high-field fMRI and single-vessel resolution optical imaging of the primary visual cortex. Neuroimage 2022; 251:118978. [PMID: 35143974 PMCID: PMC9048976 DOI: 10.1016/j.neuroimage.2022.118978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/26/2022] [Accepted: 02/05/2022] [Indexed: 11/23/2022] Open
Abstract
The mammalian neocortex exhibits a stereotypical laminar organization, with feedforward inputs arriving primarily into layer 4, local computations shaping response selectivity in layers 2/3, and outputs to other brain areas emanating via layers 2/3, 5 and 6. It cannot be assumed a priori that these signatures of laminar differences in neuronal circuitry are reflected in hemodynamic signals that form the basis of functional magnetic resonance imaging (fMRI). Indeed, optical imaging of single-vessel functional responses has highlighted the potential limits of using vascular signals as surrogates for mapping the selectivity of neural responses. Therefore, before fMRI can be employed as an effective tool for studying critical aspects of laminar processing, validation with single-vessel resolution is needed. The primary visual cortex (V1) in cats, with its precise neuronal functional micro-architecture, offers an ideal model system to examine laminar differences in stimulus selectivity across imaging modalities. Here we used cerebral blood volume weighted (wCBV) fMRI to examine if layer-specific orientation-selective responses could be detected in cat V1. We found orientation preference maps organized tangential to the cortical surface that typically extended across depth in a columnar fashion. We then examined arterial dilation and blood velocity responses to identical visual stimuli by using two- and three- photon optical imaging at single-vessel resolution-which provides a measure of the hemodynamic signals with the highest spatial resolution. Both fMRI and optical imaging revealed a consistent laminar response pattern in which orientation selectivity in cortical layer 4 was significantly lower compared to layer 2/3. This systematic change in selectivity across cortical layers has a clear underpinning in neural circuitry, particularly when comparing layer 4 to other cortical layers.
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Affiliation(s)
- Shinho Cho
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States
| | - Arani Roy
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Neuroscience, University of Minnesota, MN 55455, United States
| | - Chao J Liu
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Neuroscience, University of Minnesota, MN 55455, United States
| | - Djaudat Idiyatullin
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States
| | - Wei Zhu
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States
| | - Yi Zhang
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States
| | - Xiao-Hong Zhu
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States
| | - Phillip O'Herron
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Austin Leikvoll
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Neuroscience, University of Minnesota, MN 55455, United States
| | - Wei Chen
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States
| | - Prakash Kara
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Neuroscience, University of Minnesota, MN 55455, United States; Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29425, United States.
| | - Kâmil Uğurbil
- Center for Magnetic Resonance Research (CMRR), University of Minnesota, MN 55455, United States; Department of Radiology, University of Minnesota, MN 55455, United States.
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22
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Bollmann S, Mattern H, Bernier M, Robinson SD, Park DJ, Speck O, Polimeni JR. Imaging of the pial arterial vasculature of the human brain in vivo using high-resolution 7T time-of-flight angiography. eLife 2022; 11:71186. [PMID: 35486089 PMCID: PMC9150892 DOI: 10.7554/elife.71186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 04/28/2022] [Indexed: 11/30/2022] Open
Abstract
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 resonance angiography (TOF-MRA)—which is well suited to high 3D imaging resolutions—has not been applied to imaging the pial arteries. Here, we provide a theoretical framework that outlines how TOF-MRA can visualize small pial arteries in vivo, by employing extremely small voxels at the size of individual vessels. We then provide evidence for this theory by imaging the pial arteries at 140 µm isotropic resolution using a 7 Tesla (T) magnetic resonance imaging (MRI) scanner and prospective motion correction, and show that pial arteries one voxel width in diameter can be detected. We conclude that imaging pial arteries is not limited by slow blood flow, but instead by achievable image resolution. This study represents the first targeted, comprehensive account of imaging pial arteries in vivo in the human brain. This ultra-high-resolution angiography will enable the characterization of pial vascular anatomy across the brain to investigate patterns of blood supply and relationships between vascular and functional architecture.
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Affiliation(s)
- Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Hendrik Mattern
- Department of Biomedical Magnetic Resonance, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Michaël Bernier
- Athinoula A Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, United States
| | - Simon D Robinson
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Daniel J Park
- Athinoula A Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, United States
| | - Oliver Speck
- German Center for Neurodegenerative Diseases, Magdeburg, Germany
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23
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Yun SD, Pais-Roldán P, Palomero-Gallagher N, Shah NJ. Mapping of whole-cerebrum resting-state networks using ultra-high resolution acquisition protocols. Hum Brain Mapp 2022; 43:3386-3403. [PMID: 35384130 PMCID: PMC9248311 DOI: 10.1002/hbm.25855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 12/28/2022] Open
Abstract
Resting‐state functional magnetic resonance imaging (fMRI) has been used in numerous studies to map networks in the brain that employ spatially disparate regions. However, attempts to map networks with high spatial resolution have been hampered by conflicting technical demands and associated problems. Results from recent fMRI studies have shown that spatial resolution remains around 0.7 × 0.7 × 0.7 mm3, with only partial brain coverage. Therefore, this work aims to present a novel fMRI technique that was developed based on echo‐planar‐imaging with keyhole (EPIK) combined with repetition‐time‐external (TR‐external) EPI phase correction. Each technique has been previously shown to be effective in enhancing the spatial resolution of fMRI, and in this work, the combination of the two techniques into TR‐external EPIK provided a nominal spatial resolution of 0.51 × 0.51 × 1.00 mm3 (0.26 mm3 voxel) with whole‐cerebrum coverage. Here, the feasibility of using half‐millimetre in‐plane TR‐external EPIK for resting‐state fMRI was validated using 13 healthy subjects and the corresponding reproducible mapping of resting‐state networks was demonstrated. Furthermore, TR‐external EPIK enabled the identification of various resting‐state networks distributed throughout the brain from a single fMRI session, with mapping fidelity onto the grey matter at 7T. The high‐resolution functional image further revealed mesoscale anatomical structures, such as small cerebral vessels and the internal granular layer of the cortex within the postcentral gyrus.
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Affiliation(s)
- Seong Dae Yun
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Patricia Pais-Roldán
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Nicola Palomero-Gallagher
- Institute of Neuroscience and Medicine-1, Structural and Functional Organisation of the Brain, Forschungszentrum Jülich, Jülich, Germany.,C. & O. Vogt Institute for Brain Research, Heinrich-Heine-University, Düsseldorf, Germany.,Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen, Aachen, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany.,Institute of Neuroscience and Medicine-11, Molecular Neuroscience and Neuroimaging, JARA, Forschungszentrum Jülich, Jülich, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Department of Neurology, RWTH Aachen University, Aachen, Germany
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24
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Oliveira ÍAF, Cai Y, Hofstetter S, Siero JCW, van der Zwaag W, Dumoulin SO. Comparing BOLD and VASO-CBV population receptive field estimates in human visual cortex. Neuroimage 2021; 248:118868. [PMID: 34974115 DOI: 10.1016/j.neuroimage.2021.118868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022] Open
Abstract
Vascular Space Occupancy (VASO) is an alternative fMRI approach based on changes in Cerebral Blood Volume (CBV). VASO-CBV fMRI can provide higher spatial specificity than the blood oxygenation level-dependent (BOLD) method because the CBV response is thought to be limited to smaller vessels. To investigate how this technique compares to BOLD fMRI for cognitive neuroscience applications, we compared population receptive field (pRF) mapping estimates between BOLD and VASO-CBV. We hypothesized that VASO-CBV would elicit distinct pRF properties compared to BOLD. Specifically, since pRF size estimates also depend on vascular sources, we hypothesized that reduced vascular blurring might yield narrower pRFs for VASO-CBV measurements. We used a VASO sequence with a double readout 3D EPI sequence at 7T to simultaneously measure VASO-CBV and BOLD responses in the visual cortex while participants viewed conventional pRF mapping stimuli. Both VASO-CBV and BOLD images show similar eccentricity and polar angle maps across all participants. Compared to BOLD-based measurements, VASO-CBV yielded lower tSNR and variance explained. The pRF size changed with eccentricity similarly for VASO-CBV and BOLD, and the pRF size estimates were similar for VASO-CBV and BOLD, even when we equate variance explained between VASO-CBV and BOLD. This result suggests that the vascular component of the pRF size is not dominating in either VASO-CBV or BOLD.
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Affiliation(s)
- Ícaro A F Oliveira
- Spinoza Centre for Neuroimaging, Meibergdreef 75, Amsterdam 1105 BK, the Netherland; Experimental and Applied Psychology, VU University, Amsterdam, the Netherland.
| | - Yuxuan Cai
- Spinoza Centre for Neuroimaging, Meibergdreef 75, Amsterdam 1105 BK, the Netherland; Experimental and Applied Psychology, VU University, Amsterdam, the Netherland
| | - Shir Hofstetter
- Spinoza Centre for Neuroimaging, Meibergdreef 75, Amsterdam 1105 BK, the Netherland
| | - Jeroen C W Siero
- Spinoza Centre for Neuroimaging, Meibergdreef 75, Amsterdam 1105 BK, the Netherland; Radiology, Utrecht Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherland
| | | | - Serge O Dumoulin
- Spinoza Centre for Neuroimaging, Meibergdreef 75, Amsterdam 1105 BK, the Netherland; Experimental and Applied Psychology, VU University, Amsterdam, the Netherland; Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, the Netherland
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25
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Lacy TC, Robinson PA, Aquino KM, Pang JC. Cortical depth-dependent modeling of visual hemodynamic responses. J Theor Biol 2021; 535:110978. [PMID: 34952032 DOI: 10.1016/j.jtbi.2021.110978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/18/2021] [Accepted: 12/01/2021] [Indexed: 11/15/2022]
Abstract
A physiologically based three-dimensional (3D) hemodynamic model is developed to predict the experimentally observed blood oxygen level dependent (BOLD) responses versus the cortical depth induced by visual stimuli. Prior 2D approximations are relaxed in order to analyze 3D blood flow dynamics as a function of cortical depth. Comparison of the predictions with experimental data for evoked stimuli demonstrates that the full 3D model performs at least as well as previous approaches while remaining parsimonious. In particular, the 3D model requires significantly fewer assumptions and model parameters than previous models such that there is no longer need to define depth-specific parameter values for spatial spreading, peak amplitude, and hemodynamic velocity.
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Affiliation(s)
- Thomas C Lacy
- School of Physics, University of Sydney, New South Wales, Australia; Center for Integrative Brain Function, University of Sydney, New South Wales, Australia
| | - Peter A Robinson
- School of Physics, University of Sydney, New South Wales, Australia; Center for Integrative Brain Function, University of Sydney, New South Wales, Australia
| | - Kevin M Aquino
- School of Physics, University of Sydney, New South Wales, Australia; The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia
| | - James C Pang
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, Australia; QIMR Berghofer Medical Research Institute, Queensland, Australia.
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26
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Shao X, Guo F, Shou Q, Wang K, Jann K, Yan L, Toga AW, Zhang P, Wang DJJ. Laminar perfusion imaging with zoomed arterial spin labeling at 7 Tesla. Neuroimage 2021; 245:118724. [PMID: 34780918 PMCID: PMC8727512 DOI: 10.1016/j.neuroimage.2021.118724] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/23/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022] Open
Abstract
Laminar fMRI based on BOLD and CBV contrast at ultrahigh magnetic fields has been applied for studying the dynamics of mesoscopic brain networks. However, the quantitative interpretations of BOLD/CBV fMRI results are confounded by different baseline physiology across cortical layers. Here we introduce a novel 3D zoomed pseudo-continuous arterial spin labeling (pCASL) technique at 7T that offers the capability for quantitative measurements of laminar cerebral blood flow (CBF) both at rest and during task activation with high spatial specificity and sensitivity. We found arterial transit time in superficial layers is ∼100 ms shorter than in middle/deep layers revealing the time course of labeled blood flowing from pial arteries to downstream microvasculature. Resting state CBF peaked in the middle layers which is highly consistent with microvascular density measured from human cortex specimens. Finger tapping induced a robust two-peak laminar profile of CBF increases in the superficial (somatosensory and premotor input) and deep (spinal output) layers of M1, while finger brushing task induced a weaker CBF increase in superficial layers (somatosensory input). This observation is highly consistent with reported laminar profiles of CBV activation on M1. We further demonstrated that visuospatial attention induced a predominant CBF increase in deep layers and a smaller CBF increase on top of the lower baseline CBF in superficial layers of V1 (feedback cortical input), while stimulus driven activity peaked in the middle layers (feedforward thalamic input). With the capability for quantitative CBF measurements both at baseline and during task activation, high-resolution ASL perfusion fMRI at 7T provides an important tool for in vivo assessment of neurovascular function and metabolic activities of neural circuits across cortical layers.
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Affiliation(s)
- Xingfeng Shao
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA
| | - Fanhua Guo
- State Key Laboratory of Brain and Cognitive Science, Beijing MRI Center for Brain Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinyang Shou
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA
| | - Kai Wang
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA
| | - Kay Jann
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lirong Yan
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Peng Zhang
- State Key Laboratory of Brain and Cognitive Science, Beijing MRI Center for Brain Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Danny J J Wang
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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27
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Predicting neuronal response properties from hemodynamic responses in the auditory cortex. Neuroimage 2021; 244:118575. [PMID: 34517127 DOI: 10.1016/j.neuroimage.2021.118575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/10/2021] [Indexed: 11/22/2022] Open
Abstract
Recent functional MRI (fMRI) studies have highlighted differences in responses to natural sounds along the rostral-caudal axis of the human superior temporal gyrus. However, due to the indirect nature of the fMRI signal, it has been challenging to relate these fMRI observations to actual neuronal response properties. To bridge this gap, we present a forward model of the fMRI responses to natural sounds combining a neuronal model of the auditory cortex with physiological modeling of the hemodynamic BOLD response. Neuronal responses are modeled with a dynamic recurrent firing rate model, reflecting the tonotopic, hierarchical processing in the auditory cortex along with the spectro-temporal tradeoff in the rostral-caudal axis of its belt areas. To link modeled neuronal response properties with human fMRI data in the auditory belt regions, we generated a space of neuronal models, which differed parametrically in spectral and temporal specificity of neuronal responses. Then, we obtained predictions of fMRI responses through a biophysical model of the hemodynamic BOLD response (P-DCM). Using Bayesian model comparison, our results showed that the hemodynamic BOLD responses of the caudal belt regions in the human auditory cortex were best explained by modeling faster temporal dynamics and broader spectral tuning of neuronal populations, while rostral belt regions were best explained through fine spectral tuning combined with slower temporal dynamics. These results support the hypotheses of complementary neural information processing along the rostral-caudal axis of the human superior temporal gyrus.
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28
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Fracasso A, Dumoulin SO, Petridou N. Point-spread function of the BOLD response across columns and cortical depth in human extra-striate cortex. Prog Neurobiol 2021; 207:102187. [PMID: 34798198 DOI: 10.1016/j.pneurobio.2021.102187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Columns and layers are fundamental organizational units of the brain. Well known examples of cortical columns are the ocular dominance columns (ODCs) in primary visual cortex and the column-like stripe-based arrangement in the second visual area V2. The spatial scale of columns and layers is beyond the reach of conventional neuroimaging, but the advent of high field magnetic resonance imaging (MRI) scanners (UHF, 7 Tesla and above) has opened the possibility to acquire data at this spatial scale, in-vivo and non-invasively in humans. The most prominent non-invasive technique to measure brain function is blood oxygen level dependent (BOLD) fMRI, measuring brain activity indirectly, via changes in hemodynamics. A key determinant of the ability of high-resolution BOLD fMRI to accurately resolve columns and layers is the point-spread function (PSF) of the BOLD response in relation to the spatial extent of neuronal activity. In this study we take advantage of the stripe-based arrangement present in visual area V2, coupled with sub-millimetre anatomical and gradient-echo BOLD (GE BOLD) acquisition at 7 T to obtain PSF estimates and along cortical depth in human participants. Results show that the BOLD PSF is maximal in the superficial part of the cortex (1.78 mm), and it decreases with increasing cortical depth (0.83 mm close to white matter).
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Affiliation(s)
- Alessio Fracasso
- University of Glasgow, Institute of Neuroscience and Psychology, Glasgow, Scotland, United Kingdom.
| | - Serge O Dumoulin
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, the Netherlands; Spinoza Center for Neuroimaging, Amsterdam, the Netherlands; Experimental and Applied Psychology, VU University Amsterdam, the Netherlands
| | - Natalia Petridou
- Department of Radiology, Center for Image Sciences, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands.
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29
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Raimondo L, Knapen T, Oliveira ĹAF, Yu X, Dumoulin SO, van der Zwaag W, Siero JCW. A line through the brain: implementation of human line-scanning at 7T for ultra-high spatiotemporal resolution fMRI. J Cereb Blood Flow Metab 2021; 41:2831-2843. [PMID: 34415208 PMCID: PMC8756483 DOI: 10.1177/0271678x211037266] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Functional magnetic resonance imaging (fMRI) is a widely used tool in neuroscience to detect neurally evoked responses, e.g. the blood oxygenation level-dependent (BOLD) signal. Typically, BOLD fMRI has millimeter spatial resolution and temporal resolution of one to few seconds. To study the sub-millimeter structures and activity of the cortical gray matter, the field needs an fMRI method with high spatial and temporal resolution. Line-scanning fMRI achieves very high spatial resolution and high sampling rate, at the cost of a sacrifice in volume coverage. Here, we present a human line-scanning implementation on a 7T MRI system. First, we investigate the quality of the saturation pulses that suppress MR signal outside the line. Second, we established the best coil combination for reconstruction. Finally, we applied the line-scanning method in the occipital lobe during a visual stimulation task, showing BOLD responses along cortical depth, every 250 µm with a 200 ms repetition time (TR). We found a good correspondence of t-statistics values with 2D gradient-echo echo planar imaging (GE-EPI) BOLD fMRI data with the same temporal resolution and voxel volume (R = 0.6 ± 0.2). In summary, we demonstrate the feasibility of line-scanning in humans and this opens line-scanning fMRI for applications in cognitive and clinical neuroscience.
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Affiliation(s)
- Luisa Raimondo
- Spinoza Centre for Neuroimaging, Amsterdam, Netherlands.,Experimental and Applied Psychology, VU University, Amsterdam, Netherlands
| | - Tomas Knapen
- Spinoza Centre for Neuroimaging, Amsterdam, Netherlands.,Experimental and Applied Psychology, VU University, Amsterdam, Netherlands
| | - Ĺcaro A F Oliveira
- Spinoza Centre for Neuroimaging, Amsterdam, Netherlands.,Experimental and Applied Psychology, VU University, Amsterdam, Netherlands
| | - Xin Yu
- MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, USA
| | - Serge O Dumoulin
- Spinoza Centre for Neuroimaging, Amsterdam, Netherlands.,Experimental and Applied Psychology, VU University, Amsterdam, Netherlands.,Experimental Psychology, 8125Utrecht University, Utrecht University, Utrecht, Netherlands
| | | | - Jeroen C W Siero
- Spinoza Centre for Neuroimaging, Amsterdam, Netherlands.,Radiology, Centre for Image Sciences, University Medical Centre Utrecht, Utrecht, Netherlands
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30
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Investigating mechanisms of fast BOLD responses: The effects of stimulus intensity and of spatial heterogeneity of hemodynamics. Neuroimage 2021; 245:118658. [PMID: 34656783 DOI: 10.1016/j.neuroimage.2021.118658] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 09/18/2021] [Accepted: 10/12/2021] [Indexed: 12/17/2022] Open
Abstract
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, complementary to several existing hypotheses, that can accommodate faster fMRI dynamics beyond those predicted by the canonical model. First, we demonstrate, using both visual and somatosensory paradigms, that the timing and shape of hemodynamic response functions (HRFs) vary across graded levels of stimulus intensity-with lower-intensity stimulation eliciting faster and narrower HRFs. Second, we show that as the spatial resolution of fMRI increases, voxel-wise HRFs begin to deviate from the canonical model, with a considerable portion of voxels exhibiting faster temporal dynamics than predicted by the canonical HRF. Collectively, both stimulus/task intensity and image resolution can affect the sensitivity of fMRI to fast brain activity, which may partly explain recent observations of fast fMRI signals. It is further noteworthy that, while the present investigations focus on fast neural responses, our findings suggest that a revised hemodynamic model may benefit the many fMRI studies using paradigms with wide ranges of contrast levels (e.g., resting or naturalistic conditions) or with modern, high-resolution MR acquisitions.
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31
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Wang F, Dong Z, Wald LL, Polimeni JR, Setsompop K. Simultaneous pure T 2 and varying T 2'-weighted BOLD fMRI using Echo Planar Time-resolved Imaging for mapping cortical-depth dependent responses. Neuroimage 2021; 245:118641. [PMID: 34655771 PMCID: PMC8820652 DOI: 10.1016/j.neuroimage.2021.118641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
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 this study, we extended a recently developed distortion/blurring-free multi-shot EPI technique, Echo-Planar Time-resolved Imaging (EPTI), to cortical-depth dependent SE-fMRI at 7T to test whether it could provide purer SE BOLD contrast with minimal T2′ contamination for improved neuronal specificity. From the same acquisition, the time-resolved feature of EPTI also provides a series of asymmetric SE (ASE) images with varying T2′ weightings, and enables extraction of data equivalent to conventional SE EPI with different echo train lengths (ETLs). This allows us to systematically examine how T2′-contribution affects different SE acquisition strategies using a single dataset. A low-rank spatiotemporal subspace reconstruction was implemented for the SE-EPTI acquisition, which incorporates corrections for both shot-to-shot phase variations and dynamic B0 drifts. SE-EPTI was used in a visual task fMRI experiment to demonstrate that i) the pure SE image provided by EPTI results in the highest microvascular specificity; ii) the ASE EPTI series, with a graded introduction of T2′ weightings at time points farther away from the pure SE, show a gradual sensitivity increase along with increasing draining vein bias; iii) the longer ETL seen in conventional SE EPI acquisitions will induce more draining vein bias. Consistent results were observed across multiple subjects, demonstrating the robustness of the proposed technique for SE-BOLD fMRI with high specificity.
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Affiliation(s)
- Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA.
| | - Zijing Dong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Kawin Setsompop
- Department of Radiology, Stanford University, Stanford, USA; Department of Electrical Engineering, Stanford University, Stanford, USA
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32
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Huang P, Correia MM, Rua C, Rodgers CT, Henson RN, Carlin JD. Correcting for Superficial Bias in 7T Gradient Echo fMRI. Front Neurosci 2021; 15:715549. [PMID: 34630010 PMCID: PMC8494131 DOI: 10.3389/fnins.2021.715549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 11/29/2022] Open
Abstract
The arrival of submillimeter ultra high-field fMRI makes it possible to compare activation profiles across cortical layers. However, the blood oxygenation level dependent (BOLD) signal measured by gradient echo (GE) fMRI is biased toward superficial layers of the cortex, which is a serious confound for laminar analysis. Several univariate and multivariate analysis methods have been proposed to correct this bias. We compare these methods using computational simulations of 7T fMRI data from regions of interest (ROI) during a visual attention paradigm. We also tested the methods on a pilot dataset of human 7T fMRI data. The simulations show that two methods–the ratio of ROI means across conditions and a novel application of Deming regression–offer the most robust correction for superficial bias. Deming regression has the additional advantage that it does not require that the conditions differ in their mean activation over voxels within an ROI. When applied to the pilot dataset, we observed strikingly different layer profiles when different attention metrics were used, but were unable to discern any differences in laminar attention across layers when Deming regression or ROI ratio was applied. Our simulations demonstrates that accurate correction of superficial bias is crucial to avoid drawing erroneous conclusions from laminar analyses of GE fMRI data, and this is affirmed by the results from our pilot 7T fMRI data.
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Affiliation(s)
- Pei Huang
- Singapore Institute for Clinical Sciences, A∗STAR, Singapore, Singapore.,MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Marta M Correia
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Catarina Rua
- Wolfson Brain Imaging Centre, University of Cambridge, Cambridge, United Kingdom
| | | | - Richard N Henson
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - Johan D Carlin
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
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33
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Zoraghi M, Scherf N, Jaeger C, Sack I, Hirsch S, Hetzer S, Weiskopf N. Simulating Local Deformations in the Human Cortex Due to Blood Flow-Induced Changes in Mechanical Tissue Properties: Impact on Functional Magnetic Resonance Imaging. Front Neurosci 2021; 15:722366. [PMID: 34621151 PMCID: PMC8490675 DOI: 10.3389/fnins.2021.722366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/23/2021] [Indexed: 01/06/2023] Open
Abstract
Investigating human brain tissue is challenging due to the complexity and the manifold interactions between structures across different scales. Increasing evidence suggests that brain function and microstructural features including biomechanical features are related. More importantly, the relationship between tissue mechanics and its influence on brain imaging results remains poorly understood. As an important example, the study of the brain tissue response to blood flow could have important theoretical and experimental consequences for functional magnetic resonance imaging (fMRI) at high spatial resolutions. Computational simulations, using realistic mechanical models can predict and characterize the brain tissue behavior and give us insights into the consequent potential biases or limitations of in vivo, high-resolution fMRI. In this manuscript, we used a two dimensional biomechanical simulation of an exemplary human gyrus to investigate the relationship between mechanical tissue properties and the respective changes induced by focal blood flow changes. The model is based on the changes in the brain’s stiffness and volume due to the vasodilation evoked by neural activity. Modeling an exemplary gyrus from a brain atlas we assessed the influence of different potential mechanisms: (i) a local increase in tissue stiffness (at the level of a single anatomical layer), (ii) an increase in local volume, and (iii) a combination of both effects. Our simulation results showed considerable tissue displacement because of these temporary changes in mechanical properties. We found that the local volume increase causes more deformation and consequently higher displacement of the gyrus. These displacements introduced considerable artifacts in our simulated fMRI measurements. Our results underline the necessity to consider and characterize the tissue displacement which could be responsible for fMRI artifacts.
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Affiliation(s)
- Mahsa Zoraghi
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Nico Scherf
- Methods and Development Group Neural Data Science and Statistical Computing, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Carsten Jaeger
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Ingolf Sack
- Department of Radiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Hirsch
- Berlin Center for Advanced Neuroimaging, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Computational Neuroscience, Berlin, Germany
| | - Stefan Hetzer
- Berlin Center for Advanced Neuroimaging, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Computational Neuroscience, Berlin, Germany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,Faculty of Physics and Earth Sciences, Felix Bloch Institute for Solid State Physics, Leipzig University, Leipzig, Germany
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de Zwart JA, van Gelderen P, Duyn JH. Sensitivity limitations of high-resolution perfusion-based human fMRI at 7 Tesla. Magn Reson Imaging 2021; 84:135-144. [PMID: 34624401 DOI: 10.1016/j.mri.2021.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/07/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
The study of the brain's functional organization at laminar and columnar level of the cortex with blood oxygenation-level dependent (BOLD) functional MRI (fMRI) is affected by the contribution of large veins downstream from the microvascular response to brain activity. Blood volume- and especially perfusion-based techniques may reduce this problem because of their reduced sensitivity to venous effects, but may not allow the same spatial resolution because of smaller signal changes associated with brain activity. Here we investigated the practical resolution limits of perfusion-weighted fMRI in human visual stimulation experiments. For this purpose, we used a highly sensitive, single-shot perfusion labeling (SSPL) technique at 7 T and compared sensitivity to detect visual activation at low (2 mm, n = 10) and high (1 mm, n = 8) nominal isotropic spatial, and 3 s temporal, resolution with BOLD in 5½-minute-long experiments. Despite the smaller absolute signal change with activation, 2 mm resolution SSPL yielded comparable sensitivity to BOLD. This was attributed to a superior suppression of physiological noise with SSPL. However, at 1 mm nominal resolution, SSPL sensitivity fell on average at least 42% below that of BOLD, and detection of visual activation was compromised. This is explained by the fact that at high resolution, with both techniques, typically thermal noise rather than physiological noise dominates sensitivity. The observed sensitivity loss implies that to perform 1-mm resolution, perfusion weighted fMRI with a robustness similar to BOLD, scan times that are almost 3 times longer than the comparable BOLD experiment are required. This is in line with or slightly better than previous comparisons between perfusion-weighted fMRI and BOLD. The lower sensitivity has to be weighed against the spatial fidelity advantages of high-resolution perfusion-weighted fMRI.
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Affiliation(s)
- Jacco A de Zwart
- Advanced MRI section, Laboratory of Functional and Molecular Imaging, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Peter van Gelderen
- Advanced MRI section, Laboratory of Functional and Molecular Imaging, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jeff H Duyn
- Advanced MRI section, Laboratory of Functional and Molecular Imaging, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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Ultra-High-Field Neuroimaging Reveals Fine-Scale Processing for 3D Perception. J Neurosci 2021; 41:8362-8374. [PMID: 34413206 PMCID: PMC8496197 DOI: 10.1523/jneurosci.0065-21.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/08/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022] Open
Abstract
Binocular disparity provides critical information about three-dimensional (3D) structures to support perception and action. In the past decade significant progress has been made in uncovering human brain areas engaged in the processing of binocular disparity signals. Yet, the fine-scale brain processing underlying 3D perception remains unknown. Here, we use ultra-high-field (7T) functional imaging at submillimeter resolution to examine fine-scale BOLD fMRI signals involved in 3D perception. In particular, we sought to interrogate the local circuitry involved in disparity processing by sampling fMRI responses at different positions relative to the cortical surface (i.e., across cortical depths corresponding to layers). We tested for representations related to 3D perception by presenting participants (male and female, N = 8) with stimuli that enable stable stereoscopic perception [i.e., correlated random dot stereograms (RDS)] versus those that do not (i.e., anticorrelated RDS). Using multivoxel pattern analysis (MVPA), we demonstrate cortical depth-specific representations in areas V3A and V7 as indicated by stronger pattern responses for correlated than for anticorrelated stimuli in upper rather than deeper layers. Examining informational connectivity, we find higher feedforward layer-to-layer connectivity for correlated than anticorrelated stimuli between V3A and V7. Further, we observe disparity-specific feedback from V3A to V1 and from V7 to V3A. Our findings provide evidence for the role of V3A as a key nexus for disparity processing, which is implicated in feedforward and feedback signals related to the perceptual estimation of 3D structures.SIGNIFICANCE STATEMENT Binocular vision plays a significant role in supporting our interactions with the surrounding environment. The fine-scale neural mechanisms that underlie the brain's skill in extracting 3D structures from binocular signals are poorly understood. Here, we capitalize on recent advances in ultra-high-field functional imaging to interrogate human brain circuits involved in 3D perception at submillimeter resolution. We provide evidence for the role of area V3A as a key nexus for disparity processing, which is implicated in feedforward and feedback signals related to the perceptual estimation of 3D structures from binocular signals. These fine-scale measurements help bridge the gap between animal neurophysiology and human fMRI studies investigating cross-scale circuits, from micro circuits to global brain networks for 3D perception.
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Imaging faster neural dynamics with fast fMRI: A need for updated models of the hemodynamic response. Prog Neurobiol 2021; 207:102174. [PMID: 34525404 DOI: 10.1016/j.pneurobio.2021.102174] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 07/30/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022]
Abstract
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 nonlinear properties of the hemodynamic response that have significant implications for fast fMRI. We first review nonlinear properties of the hemodynamic response function that may underlie fast fMRI signals. We then illustrate the breakdown of canonical hemodynamic response models in the context of fast neural dynamics. We will then argue that the canonical hemodynamic response function is not likely to reflect the BOLD response to neuronal activity driven by sparse or naturalistic stimuli or perhaps to spontaneous neuronal fluctuations in the resting state. These properties suggest that fast fMRI is capable of tracking surprisingly fast neuronal dynamics, and we discuss the neuroscientific questions that could be addressed using this approach.
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Han S, Eun S, Cho H, Uludaǧ K, Kim SG. Improvement of sensitivity and specificity for laminar BOLD fMRI with double spin-echo EPI in humans at 7 T. Neuroimage 2021; 241:118435. [PMID: 34324976 DOI: 10.1016/j.neuroimage.2021.118435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
Mapping mesoscopic cortical functional units such as columns or laminae is increasingly pursued by ultra-high field (UHF) functional magnetic resonance imaging (fMRI). The most popular approach for high-resolution fMRI is currently gradient-echo (GE) blood oxygenation level-dependent (BOLD) fMRI. However, its spatial accuracy is reduced due to its sensitivity to draining vessels, including pial veins, whereas spin-echo (SE) BOLD signal is expected to have higher spatial accuracy, albeit with lower sensitivity than the GE-BOLD signal. Here, we introduce a new double spin-echo (dSE) echo-planar imaging (EPI) method to improve the sensitivity of SE-BOLD contrast by averaging two spin-echoes using three radiofrequency pulses. Human fMRI experiments were performed with slices perpendicular to the central sulcus between motor and sensory cortices at 7 T during fist-clenching with touching. First, we evaluated the feasibility of single-shot dSE-EPI for BOLD fMRI with 1.5 mm isotropic resolution and found that dSE-BOLD fMRI has higher signal-to-noise ratio (SNR), temporal SNR (tSNR), and higher functional sensitivity than conventional SE-BOLD fMRI. Second, to investigate the laminar specificity of dSE-BOLD fMRI, we implemented a multi-shot approach to achieve 0.8-mm isotropic resolution with sliding-window reconstruction. Unlike GE-BOLD fMRI, the cortical profile of dSE-BOLD fMRI peaked at ~ 1.0 mm from the surface of the primary motor and sensory cortices, demonstrating an improvement of laminar specificity in humans over GE-BOLD fMRI. The proposed multi-shot dSE-EPI method is viable for high spatial resolution UHF-fMRI studies in the pursuit of resolving mesoscopic functional units.
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Affiliation(s)
- SoHyun Han
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
| | - Seulgi Eun
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - HyungJoon Cho
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kâmil Uludaǧ
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Techna Institute & Koerner Scientist in MR Imaging, University Health Network, Toronto, Canada
| | - Seong-Gi Kim
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea.
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38
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Multivariate semi-blind deconvolution of fMRI time series. Neuroimage 2021; 241:118418. [PMID: 34303793 DOI: 10.1016/j.neuroimage.2021.118418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
Whole brain estimation of the haemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is critical to get insight on the global status of the neurovascular coupling of an individual in healthy or pathological condition. Most of existing approaches in the literature works on task-fMRI data and relies on the experimental paradigm as a surrogate of neural activity, hence remaining inoperative on resting-stage fMRI (rs-fMRI) data. To cope with this issue, recent works have performed either a two-step analysis to detect large neural events and then characterize the HRF shape or a joint estimation of both the neural and haemodynamic components in an univariate fashion. In this work, we express the neural activity signals as a combination of piece-wise constant temporal atoms associated with sparse spatial maps and introduce an haemodynamic parcellation of the brain featuring a temporally dilated version of a given HRF model in each parcel with unknown dilation parameters. We formulate the joint estimation of the HRF shapes and spatio-temporal neural representations as a multivariate semi-blind deconvolution problem in a paradigm-free setting and introduce constraints inspired from the dictionary learning literature to ease its identifiability. A fast alternating minimization algorithm, along with its efficient implementation, is proposed and validated on both synthetic and real rs-fMRI data at the subject level. To demonstrate its significance at the population level, we apply this new framework to the UK Biobank data set, first for the discrimination of haemodynamic territories between balanced groups (n=24 individuals in each) patients with an history of stroke and healthy controls and second, for the analysis of normal aging on the neurovascular coupling. Overall, we statistically demonstrate that a pathology like stroke or a condition like normal brain aging induce longer haemodynamic delays in certain brain areas (e.g. Willis polygon, occipital, temporal and frontal cortices) and that this haemodynamic feature may be predictive with an accuracy of 74 % of the individual's age in a supervised classification task performed on n=459 subjects.
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Yang J, Huber L, Yu Y, Bandettini PA. Linking cortical circuit models to human cognition with laminar fMRI. Neurosci Biobehav Rev 2021; 128:467-478. [PMID: 34245758 DOI: 10.1016/j.neubiorev.2021.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Laboratory animal research has provided significant knowledge into the function of cortical circuits at the laminar level, which has yet to be fully leveraged towards insights about human brain function on a similar spatiotemporal scale. The use of functional magnetic resonance imaging (fMRI) in conjunction with neural models provides new opportunities to gain important insights from current knowledge. During the last five years, human studies have demonstrated the value of high-resolution fMRI to study laminar-specific activity in the human brain. This is mostly performed at ultra-high-field strengths (≥ 7 T) and is known as laminar fMRI. Advancements in laminar fMRI are beginning to open new possibilities for studying questions in basic cognitive neuroscience. In this paper, we first review recent methodological advances in laminar fMRI and describe recent human laminar fMRI studies. Then, we discuss how the use of laminar fMRI can help bridge the gap between cortical circuit models and human cognition.
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Affiliation(s)
- Jiajia Yang
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan; Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA.
| | - Laurentius Huber
- MR-Methods Group, Faculty of Psychology and Neuroscience, University of Maastricht, Maastricht, the Netherlands
| | - Yinghua Yu
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan; Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA
| | - Peter A Bandettini
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA; Functional MRI Core Facility, National Institute of Mental Health, Bethesda, MD, USA
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40
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Frässle S, Aponte EA, Bollmann S, Brodersen KH, Do CT, Harrison OK, Harrison SJ, Heinzle J, Iglesias S, Kasper L, Lomakina EI, Mathys C, Müller-Schrader M, Pereira I, Petzschner FH, Raman S, Schöbi D, Toussaint B, Weber LA, Yao Y, Stephan KE. TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatry. Front Psychiatry 2021; 12:680811. [PMID: 34149484 PMCID: PMC8206497 DOI: 10.3389/fpsyt.2021.680811] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Abstract
Psychiatry faces fundamental challenges with regard to mechanistically guided differential diagnosis, as well as prediction of clinical trajectories and treatment response of individual patients. This has motivated the genesis of two closely intertwined fields: (i) Translational Neuromodeling (TN), which develops "computational assays" for inferring patient-specific disease processes from neuroimaging, electrophysiological, and behavioral data; and (ii) Computational Psychiatry (CP), with the goal of incorporating computational assays into clinical decision making in everyday practice. In order to serve as objective and reliable tools for clinical routine, computational assays require end-to-end pipelines from raw data (input) to clinically useful information (output). While these are yet to be established in clinical practice, individual components of this general end-to-end pipeline are being developed and made openly available for community use. In this paper, we present the Translational Algorithms for Psychiatry-Advancing Science (TAPAS) software package, an open-source collection of building blocks for computational assays in psychiatry. Collectively, the tools in TAPAS presently cover several important aspects of the desired end-to-end pipeline, including: (i) tailored experimental designs and optimization of measurement strategy prior to data acquisition, (ii) quality control during data acquisition, and (iii) artifact correction, statistical inference, and clinical application after data acquisition. Here, we review the different tools within TAPAS and illustrate how these may help provide a deeper understanding of neural and cognitive mechanisms of disease, with the ultimate goal of establishing automatized pipelines for predictions about individual patients. We hope that the openly available tools in TAPAS will contribute to the further development of TN/CP and facilitate the translation of advances in computational neuroscience into clinically relevant computational assays.
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Affiliation(s)
- Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Eduardo A. Aponte
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Saskia Bollmann
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, United States
- Department of Radiology, Harvard Medical School, Charlestown, MA, United States
| | - Kay H. Brodersen
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Cao T. Do
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Olivia K. Harrison
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Samuel J. Harrison
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jakob Heinzle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Sandra Iglesias
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Lars Kasper
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Techna Institute, University Health Network, Toronto, ON, Canada
| | - Ekaterina I. Lomakina
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Christoph Mathys
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Interacting Minds Center, Aarhus University, Aarhus, Denmark
| | - Matthias Müller-Schrader
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Inês Pereira
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Frederike H. Petzschner
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Sudhir Raman
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Dario Schöbi
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Birte Toussaint
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Lilian A. Weber
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Yu Yao
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Klaas E. Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
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Pfaffenrot V, Voelker MN, Kashyap S, Koopmans PJ. Laminar fMRI using T 2-prepared multi-echo FLASH. Neuroimage 2021; 236:118163. [PMID: 34023449 DOI: 10.1016/j.neuroimage.2021.118163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
Functional magnetic resonance imaging (fMRI) using blood oxygenation level dependent (BOLD) contrast at a sub-millimeter scale is a promising technique to probe neural activity at the level of cortical layers. While gradient echo (GRE) BOLD sequences exhibit the highest sensitivity, their signal is confounded by unspecific extravascular (EV) and intravascular (IV) effects of large intracortical ascending veins and pial veins leading to a downstream blurring effect of local signal changes. In contrast, spin echo (SE) fMRI promises higher specificity towards signal changes near the microvascular compartment. However, the T2-weighted signal is typically sampled with a gradient echo readout imposing additional T2'-weighting. In this work, we used a T2-prepared (T2-prep) sequence with short GRE readouts to investigate its capability to acquire laminar fMRI data during a visual task in humans at 7 T. By varying the T2-prep echo time (TEprep) and acquiring multiple gradient echoes (TEGRE) per excitation, we studied the specificity of the sequence and the influence of possible confounding contributions to the shape of laminar fMRI profiles. By fitting and extrapolating the multi-echo GRE data to a TEGRE = 0 ms condition, we show for the first time laminar profiles free of T2'-pollution, confined to gray matter. This finding is independent of TEprep, except for the shortest one (31 ms) where hints of a remaining intravascular component can be seen. For TEGRE > 0 ms a prominent peak at the pial surface is observed that increases with longer TEGRE and dominates the shape of the profiles independent of the amount of T2-weighting. Simulations show that the peak at the pial surface is a result of static EV dephasing around pial vessels in CSF visible in GM due to partial voluming. Additionally, another, weaker, static dephasing effect is observed throughout all layers of the cortex, which is particularly obvious in the data with shortest T2-prep echo time. Our simulations show that this cannot be explained by intravascular dephasing but that it is likely caused by extravascular effects of the intracortical and pial veins. We conclude that even for TEGRE as short as 2.3 ms, the T2'-weighting added to the T2-weighting is enough to dramatically affect the laminar specificity of the BOLD signal change. However, the bulk of this corruption stems from CSF partial volume effects which can in principle be addressed by increasing the spatial resolution of the acquisition.
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Affiliation(s)
- Viktor Pfaffenrot
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University of Duisburg-Essen, 45141 Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
| | - Maximilian N Voelker
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University of Duisburg-Essen, 45141 Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Sriranga Kashyap
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, 6229 Maastricht, Netherlands
| | - Peter J Koopmans
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University of Duisburg-Essen, 45141 Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
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42
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Uludag K, Havlicek M. Determining laminar neuronal activity from BOLD fMRI using a generative model. Prog Neurobiol 2021; 207:102055. [PMID: 33930519 DOI: 10.1016/j.pneurobio.2021.102055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/12/2021] [Accepted: 04/20/2021] [Indexed: 11/17/2022]
Abstract
Laminar fMRI using the BOLD contrast enables the non-invasive investigation of mesoscopic functional circuits in the human brain. However, the laminar neuronal activity is spatiotemporally biased in the observed cortical depth profiles of the BOLD signal. In this study, we propose a generative fMRI signal model, comprehensively covering the relationship between cortical depth-dependent changes in excitatory and inhibitory neuronal activity with the sampling of the BOLD signal with finite voxels. The generative model allowed us to investigate pertinent questions regarding the accuracy of the laminar BOLD signal relative to the neuronal activity, and we found that: a) condition differences in laminar BOLD signals may be more reflective of neuronal activity than single condition BOLD signal depth profiles; b) angular dependence of the BOLD signal induces significant signal variability, which can mask underlying activity profiles; c) even if only three neuronal depths are of interest, more BOLD signal depths should be considered in the analysis. In addition, we recommend that the laminar BOLD data should be displayed using the centroid method to appreciate its spatial distribution in the original resolution. Finally, we showed that Bayesian model inversion of the generative model can improve sensitivity and specificity of assessing depth-dependent neuronal changes both for steady-state and dynamically.
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Affiliation(s)
- Kamil Uludag
- Techna Institute & Koerner Scientist in MR Imaging, University Health Network, Toronto, Canada; Center for Neuroscience Imaging Research, Institute for Basic Science & Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
| | - Martin Havlicek
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
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43
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Bennett MR, Farnell L, Gibson WG. Quantitative relations between BOLD responses, cortical energetics and impulse firing across cortical depth. Eur J Neurosci 2021; 54:4230-4245. [PMID: 33901325 DOI: 10.1111/ejn.15247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
The blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signal arises as a consequence of changes in cerebral blood flow (CBF) and cerebral metabolic rate of oxygen ( CMR O 2 ) that in turn are modulated by changes in neural activity. Recent advances in imaging have achieved sub-millimetre resolution and allowed investigation of the BOLD response as a function of cortical depth. Here, we adapt our previous theory relating the BOLD signal to neural activity to produce a quantitative model that incorporates venous blood draining between cortical layers. The adjustable inputs to the model are the neural activity and a parameter governing this blood draining. A three-layer version for transient neural inputs and a multi-layer version for constant or tonic neural inputs are able to account for a variety of experimental results, including negative BOLD signals.
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Affiliation(s)
- Maxwell R Bennett
- Brain and Mind Research Centre, University of Sydney, Camperdown, NSW, Australia
- Center for Mathematical Biology, University of Sydney, Sydney, NSW, Australia
| | - Leslie Farnell
- Center for Mathematical Biology, University of Sydney, Sydney, NSW, Australia
- The School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - William G Gibson
- Center for Mathematical Biology, University of Sydney, Sydney, NSW, Australia
- The School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
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Kashyap S, Ivanov D, Havlicek M, Huber L, Poser BA, Uludağ K. Sub-millimetre resolution laminar fMRI using Arterial Spin Labelling in humans at 7 T. PLoS One 2021; 16:e0250504. [PMID: 33901230 PMCID: PMC8075193 DOI: 10.1371/journal.pone.0250504] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
Laminar fMRI at ultra-high magnetic field strength is typically carried out using the Blood Oxygenation Level-Dependent (BOLD) contrast. Despite its unrivalled sensitivity to detecting activation, the BOLD contrast is limited in its spatial specificity due to signals stemming from intra-cortical ascending and pial veins. Alternatively, regional changes in perfusion (i.e., cerebral blood flow through tissue) are colocalised to neuronal activation, which can be non-invasively measured using Arterial Spin Labelling (ASL) MRI. In addition, ASL provides a quantitative marker of neuronal activation in terms of perfusion signal, which is simultaneously acquired along with the BOLD signal. However, ASL for laminar imaging is challenging due to the lower SNR of the perfusion signal and higher RF power deposition i.e., specific absorption rate (SAR) of ASL sequences. In the present study, we present for the first time in humans, isotropic sub-millimetre spatial resolution functional perfusion images using Flow-sensitive Alternating Inversion Recovery (FAIR) ASL with a 3D-EPI readout at 7 T. We show that robust statistical activation maps can be obtained with perfusion-weighting in a single session. We observed the characteristic BOLD amplitude increase towards the superficial laminae, and, in apparent discrepancy, the relative perfusion profile shows a decrease of the amplitude and the absolute perfusion profile a much smaller increase towards the cortical surface. Considering the draining vein effect on the BOLD signal using model-based spatial “convolution”, we show that the empirically measured perfusion and BOLD profiles are, in fact, consistent with each other. This study demonstrates that laminar perfusion fMRI in humans is feasible at 7 T and that caution must be exercised when interpreting BOLD signal laminar profiles as direct representation of the cortical distribution of neuronal activity.
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Affiliation(s)
- Sriranga Kashyap
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Maastricht Brain Imaging Centre (M-BIC), Maastricht University, Maastricht, The Netherlands
- * E-mail: (SK); (DI)
| | - Dimo Ivanov
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Maastricht Brain Imaging Centre (M-BIC), Maastricht University, Maastricht, The Netherlands
- * E-mail: (SK); (DI)
| | - Martin Havlicek
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Laurentius Huber
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Maastricht Brain Imaging Centre (M-BIC), Maastricht University, Maastricht, The Netherlands
| | - Benedikt A. Poser
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Maastricht Brain Imaging Centre (M-BIC), Maastricht University, Maastricht, The Netherlands
| | - Kâmil Uludağ
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
- Department of Biomedical Engineering, N Center, Sungkyunkwan University, Suwon, South Korea
- Techna Institute & Koerner Scientist in MR Imaging, University Health Network, Toronto, Canada
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Fracasso A, Dumoulin SO, Petridou N. Point-spread function of the BOLD response across columns and cortical depth in human extra-striate cortex. Prog Neurobiol 2021; 202:102034. [PMID: 33741401 DOI: 10.1016/j.pneurobio.2021.102034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/08/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Columns and layers are fundamental organizational units of the brain. Well known examples of cortical columns are the ocular dominance columns (ODCs) in primary visual cortex and the column-like stripe-based arrangement in the second visual area V2. The spatial scale of columns and layers is beyond the reach of conventional neuroimaging, but the advent of high field magnetic resonance imaging (MRI) scanners (UHF, 7 T and above) has opened the possibility to acquire data at this spatial scale, in-vivo and non-invasively in humans. The most prominent non-invasive technique to measure brain function is blood oxygen level dependent (BOLD) fMRI, measuring brain activity indirectly, via changes in hemodynamics. A key determinant of the ability of high-resolution BOLD fMRI to accurately resolve columns and layers is the point-spread function (PSF) of the BOLD response in relation to the spatial extent of neuronal activity. In this study we take advantage of the stripe-based arrangement present in visual area V2, coupled with sub-millimetre anatomical and gradient-echo BOLD (GE BOLD) acquisition at 7 T to obtain PSF estimates and along cortical depth in human participants. Results show that the BOLD PSF is maximal in the superficial part of the cortex (1.78 mm), and it decreases with increasing cortical depth (0.83 mm close to white matter).
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Affiliation(s)
- Alessio Fracasso
- University of Glasgow, Institute of Neuroscience and Psychology, Glasgow, Scotland, United Kingdom.
| | - Serge O Dumoulin
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, the Netherlands; Spinoza Center for Neuroimaging, Amsterdam, the Netherlands; Experimental and Applied Psychology, VU University Amsterdam, the Netherlands
| | - Natalia Petridou
- Department of Radiology, Center for Image Sciences, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands.
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Tsvetanov KA, Henson RNA, Rowe JB. Separating vascular and neuronal effects of age on fMRI BOLD signals. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190631. [PMID: 33190597 PMCID: PMC7741031 DOI: 10.1098/rstb.2019.0631] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
Accurate identification of brain function is necessary to understand the neurobiology of cognitive ageing, and thereby promote well-being across the lifespan. A common tool used to investigate neurocognitive ageing is functional magnetic resonance imaging (fMRI). However, although fMRI data are often interpreted in terms of neuronal activity, the blood oxygenation level-dependent (BOLD) signal measured by fMRI includes contributions of both vascular and neuronal factors, which change differentially with age. While some studies investigate vascular ageing factors, the results of these studies are not well known within the field of neurocognitive ageing and therefore vascular confounds in neurocognitive fMRI studies are common. Despite over 10 000 BOLD-fMRI papers on ageing, fewer than 20 have applied techniques to correct for vascular effects. However, neurovascular ageing is not only a confound in fMRI, but an important feature in its own right, to be assessed alongside measures of neuronal ageing. We review current approaches to dissociate neuronal and vascular components of BOLD-fMRI of regional activity and functional connectivity. We highlight emerging evidence that vascular mechanisms in the brain do not simply control blood flow to support the metabolic needs of neurons, but form complex neurovascular interactions that influence neuronal function in health and disease. This article is part of the theme issue 'Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.
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Affiliation(s)
- Kamen A. Tsvetanov
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0SZ, UK
- Department of Psychology, University of Cambridge, Cambridge CB2 3EB, UK
| | - Richard N. A. Henson
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SP, UK
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - James B. Rowe
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0SZ, UK
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
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Weldon KB, Olman CA. Forging a path to mesoscopic imaging success with ultra-high field functional magnetic resonance imaging. Philos Trans R Soc Lond B Biol Sci 2020; 376:20200040. [PMID: 33190599 PMCID: PMC7741029 DOI: 10.1098/rstb.2020.0040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Functional magnetic resonance imaging (fMRI) studies with ultra-high field (UHF, 7+ Tesla) technology enable the acquisition of high-resolution images. In this work, we discuss recent achievements in UHF fMRI at the mesoscopic scale, on the order of cortical columns and layers, and examine approaches to addressing common challenges. As researchers push to smaller and smaller voxel sizes, acquisition and analysis decisions have greater potential to degrade spatial accuracy, and UHF fMRI data must be carefully interpreted. We consider the impact of acquisition decisions on the spatial specificity of the MR signal with a representative dataset with 0.8 mm isotropic resolution. We illustrate the trade-offs in contrast with noise ratio and spatial specificity of different acquisition techniques and show that acquisition blurring can increase the effective voxel size by as much as 50% in some dimensions. We further describe how different sources of degradations to spatial resolution in functional data may be characterized. Finally, we emphasize that progress in UHF fMRI depends not only on scientific discovery and technical advancement, but also on informal discussions and documentation of challenges researchers face and overcome in pursuit of their goals. This article is part of the theme issue 'Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.
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Affiliation(s)
- Kimberly B Weldon
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN 55455, USA.,Center for Magnetic Resonance Imaging, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cheryl A Olman
- Center for Magnetic Resonance Imaging, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Psychology, University of Minnesota, Minneapolis, MN 55455, USA
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Zamboni E, Kemper VG, Goncalves NR, Jia K, Karlaftis VM, Bell SJ, Giorgio J, Rideaux R, Goebel R, Kourtzi Z. Fine-scale computations for adaptive processing in the human brain. eLife 2020; 9:e57637. [PMID: 33170124 PMCID: PMC7688307 DOI: 10.7554/elife.57637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/09/2020] [Indexed: 12/02/2022] Open
Abstract
Adapting to the environment statistics by reducing brain responses to repetitive sensory information is key for efficient information processing. Yet, the fine-scale computations that support this adaptive processing in the human brain remain largely unknown. Here, we capitalise on the sub-millimetre resolution of ultra-high field imaging to examine functional magnetic resonance imaging signals across cortical depth and discern competing hypotheses about the brain mechanisms (feedforward vs. feedback) that mediate adaptive processing. We demonstrate layer-specific suppressive processing within visual cortex, as indicated by stronger BOLD decrease in superficial and middle than deeper layers for gratings that were repeatedly presented at the same orientation. Further, we show altered functional connectivity for adaptation: enhanced feedforward connectivity from V1 to higher visual areas, short-range feedback connectivity between V1 and V2, and long-range feedback occipito-parietal connectivity. Our findings provide evidence for a circuit of local recurrent and feedback interactions that mediate rapid brain plasticity for adaptive information processing.
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Affiliation(s)
- Elisa Zamboni
- Department of Psychology, University of CambridgeCambridgeUnited Kingdom
| | - Valentin G Kemper
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht UniversityMaastrichtNetherlands
- Department of Cognitive Neuroscience, Maastricht Brain Imaging Center, Maastricht UniversityMaastrichtNetherlands
| | | | - Ke Jia
- Department of Psychology, University of CambridgeCambridgeUnited Kingdom
| | | | - Samuel J Bell
- Department of Psychology, University of CambridgeCambridgeUnited Kingdom
| | - Joseph Giorgio
- Department of Psychology, University of CambridgeCambridgeUnited Kingdom
| | - Reuben Rideaux
- Department of Psychology, University of CambridgeCambridgeUnited Kingdom
| | - Rainer Goebel
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht UniversityMaastrichtNetherlands
- Department of Cognitive Neuroscience, Maastricht Brain Imaging Center, Maastricht UniversityMaastrichtNetherlands
| | - Zoe Kourtzi
- Department of Psychology, University of CambridgeCambridgeUnited Kingdom
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Navarro KT, Sanchez MJ, Engel SA, Olman CA, Weldon KB. Depth-dependent functional MRI responses to chromatic and achromatic stimuli throughout V1 and V2. Neuroimage 2020; 226:117520. [PMID: 33137474 PMCID: PMC7958868 DOI: 10.1016/j.neuroimage.2020.117520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
In the primate visual system, form (shape, location) and color information are processed in separate but interacting pathways. Recent access to high-resolution neuroimaging has facilitated the exploration of the structure of these pathways at the mesoscopic level in the human visual cortex. We used 7T fMRI to observe selective activation of the primary visual cortex to chromatic versus achromatic stimuli in five participants across two scanning sessions. Achromatic checkerboards with low spatial frequency and high temporal frequency targeted the color-insensitive magnocellular pathway. Chromatic checkerboards with higher spatial frequency and low temporal frequency targeted the color-selective parvocellular pathway. This work resulted in three main findings. First, responses driven by chromatic stimuli had a laminar profile biased towards superficial layers of V1, as compared to responses driven by achromatic stimuli. Second, we found stronger preference for chromatic stimuli in parafoveal V1 compared with peripheral V1. Finally, we found alternating, stimulus-selective bands stemming from the V1 border into V2 and V3. Similar alternating patterns have been previously found in both NHP and human extrastriate cortex. Together, our findings confirm the utility of fMRI for revealing details of mesoscopic neural architecture in human cortex.
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Affiliation(s)
- Karen T Navarro
- Department of Psychology, University of Minnesota, 75 E River Rd, Minneapolis, MN 55455, United States.
| | - Marisa J Sanchez
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, 2450 Riverside Ave f275, Minneapolis, MN 55454, United States
| | - Stephen A Engel
- Department of Psychology, University of Minnesota, 75 E River Rd, Minneapolis, MN 55455, United States
| | - Cheryl A Olman
- Department of Psychology, University of Minnesota, 75 E River Rd, Minneapolis, MN 55455, United States; Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN 55455, United States
| | - Kimberly B Weldon
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, 2450 Riverside Ave f275, Minneapolis, MN 55454, United States; Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN 55455, United States
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50
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Bollmann S, Barth M. New acquisition techniques and their prospects for the achievable resolution of fMRI. Prog Neurobiol 2020; 207:101936. [PMID: 33130229 DOI: 10.1016/j.pneurobio.2020.101936] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/10/2020] [Accepted: 10/18/2020] [Indexed: 01/17/2023]
Abstract
This work reviews recent advances in technologies for functional magnetic resonance imaging (fMRI) of the human brain and highlights the push for higher functional specificity based on increased spatial resolution and specific MR contrasts to reveal previously undetectable functional properties of small-scale cortical structures. We discuss how the combination of MR hardware, advanced acquisition techniques and various MR contrast mechanisms have enabled recent progress in functional neuroimaging. However, these advanced fMRI practices have only been applied to a handful of neuroscience questions to date, with the majority of the neuroscience community still using conventional imaging techniques. We thus discuss upcoming challenges and possibilities for fMRI technology development in human neuroscience. We hope that readers interested in functional brain imaging acquire an understanding of current and novel developments and potential future applications, even if they don't have a background in MR physics or engineering. We summarize the capabilities of standard fMRI acquisition schemes with pointers to relevant literature and comprehensive reviews and introduce more recent developments.
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Affiliation(s)
- Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Markus Barth
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia; School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Australia; ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, QLD, Australia.
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