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Iyyappan Valsala P, Veldmann M, Bosch D, Scheffler K, Ehses P. Submillimeter balanced SSFP BOLD-functional MRI accelerated with 3D stack-of-spirals at 9.4 T. Magn Reson Med 2024; 92:186-201. [PMID: 38440956 DOI: 10.1002/mrm.30064] [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: 10/19/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE This work aims to improve the speed of balanced SSFP (bSSFP) acquisition with segmented 3D stack-of-spirals for functional brain studies at ultrahigh field. METHODS Functional experiments were performed with an accelerated 3D stack-of-spirals sequence with water excitation for fat suppression. The resulting data were reconstructed using an iterative algorithm with corrections for system imperfections such as trajectory deviations and B0 inhomogeneity. In the first set of experiments, we evaluated the signal change and stability with respect to echo and TR for a full-field checkerboard stimulus. To demonstrate the high spatio-temporal resolution of the developed method, the results of three optimized protocols at submillimeter resolution (0.6-mm isotropic and 0.8-mm isotropic) and at 1.2 mm isotropic resolution for whole-brain coverage were shown. RESULTS Water excitation and the model-based iterative reconstruction improved image quality. The BOLD-related signal changes increased with longer TE and longer TR. We observed an increase in thermal noise performance at lower TE and higher TR. However, signal stability deteriorates at higher TE and TR. Therefore, optimized protocols used shorter TE and moderately long TR to maximize the sensitivity and speed. Reproducible activations were detected along the gray-matter gyri in the submillimeter protocols with a median signal change of approximately 4% across subjects. CONCLUSIONS Three-dimensional stack-of-spirals enables passband balanced SSFP functional imaging at a much higher spatial and temporal scale, compared with conventional spoiled gradient-echo train sequences.
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Affiliation(s)
| | - Marten Veldmann
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dario Bosch
- Magnetic Resonance Center, Max-Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Klaus Scheffler
- Magnetic Resonance Center, Max-Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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Báez-Yáñez MG, Siero JCW, Curcic V, van Osch MJP, Petridou N. On the influence of the vascular architecture on Gradient Echo and Spin Echo BOLD fMRI signals across cortical depth: a simulation approach based on realistic 3D vascular networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596593. [PMID: 38853905 PMCID: PMC11160811 DOI: 10.1101/2024.05.30.596593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
GE-BOLD contrast stands out as the predominant technique in functional MRI experiments for its high sensitivity and straightforward implementation. GE-BOLD exhibits rather similar sensitivity to vessels independent of their size at submillimeter resolution studies like those examining cortical columns and laminae. However, the presence of nonspecific macrovascular contributions poses a challenge to accurately isolate neuronal activity. SE-BOLD increases specificity towards small vessels, thereby enhancing its specificity to neuronal activity, due to the effective suppression of extravascular contributions caused by macrovessels with its refocusing pulse. However, even SE-BOLD measurements may not completely remove these macrovascular contributions. By simulating hemodynamic signals across cortical depth, we gain insights into vascular contributions to the laminar BOLD signal. In this study, we employed four realistic 3D vascular models to simulate oxygen saturation states in various vascular compartments, aiming to characterize both intravascular and extravascular contributions to GE and SE signals, and corresponding BOLD signal changes, across cortical depth at 7T. Simulations suggest that SE-BOLD cannot completely reduce the macrovascular contribution near the pial surface. Simulations also show that both the specificity and signal amplitude of BOLD signals at 7T depend on the spatial arrangement of large vessels throughout cortical depth and on the pial surface.
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Affiliation(s)
- Mario Gilberto Báez-Yáñez
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeroen C W Siero
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
- Spinoza Centre for Neuroimaging Amsterdam, Amsterdam, the Netherlands
| | - Vanja Curcic
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthias J P van Osch
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Natalia Petridou
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
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Báez-Yáñez MG, Schellekens W, Bhogal AA, Roefs ECA, van Osch MJP, Siero JCW, Petridou N. A fully synthetic three-dimensional human cerebrovascular model based on histological characteristics to investigate the hemodynamic fingerprint of the layer BOLD fMRI signal formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595716. [PMID: 38826311 PMCID: PMC11142244 DOI: 10.1101/2024.05.24.595716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Recent advances in functional magnetic resonance imaging (fMRI) at ultra-high field (≥7 tesla), novel hardware, and data analysis methods have enabled detailed research on neurovascular function, such as cortical layer-specific activity, in both human and nonhuman species. A widely used fMRI technique relies on the blood oxygen level-dependent (BOLD) signal. BOLD fMRI offers insights into brain function by measuring local changes in cerebral blood volume, cerebral blood flow, and oxygen metabolism induced by increased neuronal activity. Despite its potential, interpreting BOLD fMRI data is challenging as it is only an indirect measurement of neuronal activity. Computational modeling can help interpret BOLD data by simulating the BOLD signal formation. Current developments have focused on realistic 3D vascular models based on rodent data to understand the spatial and temporal BOLD characteristics. While such rodent-based vascular models highlight the impact of the angioarchitecture on the BOLD signal amplitude, anatomical differences between the rodent and human vasculature necessitate the development of human-specific models. Therefore, a computational framework integrating human cortical vasculature, hemodynamic changes, and biophysical properties is essential. Here, we present a novel computational approach: a three-dimensional VAscular MOdel based on Statistics (3D VAMOS), enabling the investigation of the hemodynamic fingerprint of the BOLD signal within a model encompassing a fully synthetic human 3D cortical vasculature and hemodynamics. Our algorithm generates microvascular and macrovascular architectures based on morphological and topological features from the literature on human cortical vasculature. By simulating specific oxygen saturation states and biophysical interactions, our framework characterizes the intravascular and extravascular signal contributions across cortical depth and voxel-wise levels for gradient-echo and spin-echo readouts. Thereby, the 3D VAMOS computational framework demonstrates that using human characteristics significantly affects the BOLD fingerprint, making it an essential step in understanding the fundamental underpinnings of layer-specific fMRI experiments.
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Affiliation(s)
- Mario Gilberto Báez-Yáñez
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter Schellekens
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
- Donders Centre for Cognitive Neuroimaging, Radboud UMC, Nijmegen, Netherlands
| | - Alex A Bhogal
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emiel C A Roefs
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthias J P van Osch
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen C W Siero
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
- Spinoza Centre for Neuroimaging Amsterdam, Amsterdam, the Netherlands
| | - Natalia Petridou
- Translational Neuroimaging Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, the Netherlands
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Dresbach S, Huber R, Gulban OF, Pizzuti A, Trampel R, Ivanov D, Weiskopf N, Goebel R. Characterisation of laminar and vascular spatiotemporal dynamics of CBV and BOLD signals using VASO and ME-GRE at 7T in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.576050. [PMID: 38410457 PMCID: PMC10896347 DOI: 10.1101/2024.01.25.576050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Interpretation of cortical laminar functional magnetic resonance imaging (fMRI) activity requires detailed knowledge of the spatiotemporal haemodynamic response across vascular compartments due to the well-known vascular biases (e.g. the draining veins). Further complications arise from the spatiotemporal hemodynamic response that differs depending on the duration of stimulation. This information is crucial for future studies using depth-dependent cerebral blood volume (CBV) measurements, which promise higher specificity for the cortical microvasculature than the blood oxygenation level dependent (BOLD) contrast. To date, direct information about CBV dynamics with respect to stimulus duration, cortical depth and vasculature is missing in humans. Therefore, we characterized the cortical depth-dependent CBV-haemodynamic responses across a wide set of stimulus durations with 0.9 mm isotropic spatial and 0.785 seconds effective temporal resolution in humans using slice-selective slab-inversion vascular space occupancy (SS-SI VASO). Additionally, we investigated signal contributions from macrovascular compartments using fine-scale vascular information from multi-echo gradient-echo (ME-GRE) data at 0.35 mm isotropic resolution. In total, this resulted in >7.5h of scanning per participant (n=5). We have three major findings: (I) While we could demonstrate that 1 second stimulation is viable using VASO, more than 12 seconds stimulation provides better CBV responses in terms of specificity to microvasculature, but durations beyond 24 seconds of stimulation may be wasteful for certain applications. (II) We observe that CBV responses show dilation patterns across the cortex. (III) While we found increasingly strong BOLD signal responses in vessel-dominated voxels with longer stimulation durations, we found increasingly strong CBV signal responses in vessel-dominated voxels only until 4 second stimulation durations. After 4 seconds, only the signal from non-vessel dominated voxels kept increasing. This might explain why CBV responses are more specific to the underlying neuronal activity for long stimulus durations.
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Affiliation(s)
- Sebastian Dresbach
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Renzo Huber
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
- National Institutes of Health, Bethesda, MD, USA
| | - Omer Faruk Gulban
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
- Brain innovation, Maastricht, the Netherlands
| | - Alessandra Pizzuti
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
- Brain innovation, Maastricht, the Netherlands
| | - Robert Trampel
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Dimo Ivanov
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth System Sciences, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, 12 Queen Square, London WC1N 3AR, UK
| | - Rainer Goebel
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
- Brain innovation, Maastricht, the Netherlands
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Domingos C, Fouto AR, Nunes RG, Ruiz-Tagle A, Esteves I, Silva NA, Vilela P, Gil-Gouveia R, Figueiredo P. Impact of susceptibility-induced distortion correction on perfusion imaging by pCASL with a segmented 3D GRASE readout. Magn Reson Imaging 2023:S0730-725X(23)00104-2. [PMID: 37343905 DOI: 10.1016/j.mri.2023.06.010] [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: 02/07/2023] [Revised: 05/18/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
PURPOSE The consensus for the clinical implementation of arterial spin labeling (ASL) perfusion imaging recommends a segmented 3D Gradient and Spin-Echo (GRASE) readout for optimal signal-to-noise-ratio(SNR). The correction of the associated susceptibility-induced geometric distortions has been shown to improve diagnostic precision, but its impact on ASL data has not been systematically assessed and it is not consistently part of pre-processing pipelines. Here, we investigate the effects of susceptibility-induced distortion correction on perfusion imaging by pseudo-continuous ASL (pCASL) with a segmented 3D GRASE readout. METHODS Data acquired from 28 women using pCASL with 3D GRASE at 3T was analyzed using three pre-processing options: without distortion correction, with distortion correction, and with spatial smoothing (without distortion correction) matched to control for blurring effects induced by distortion correction. Maps of temporal SNR (tSNR) and relative perfusion were analyzed in eight regions-of-interest (ROIs) across the brain. RESULTS Distortion correction significantly affected tSNR and relative perfusion across the brain. Increases in tSNR were like those produced by matched spatial smoothing in most ROIs, indicating that they were likely due to blurring effects. However, that was not the case in the frontal and temporal lobes, where we also found increased relative perfusion with distortion correction even compared with matched spatial smoothing. These effects were found in both controls and patients, with no interactions with the participant group. CONCLUSION Correction of Susceptibility-induced distortions significantly impacts ASL perfusion imaging using a segmented 3D GRASE readout, and this step should therefore be considered in ASL pre-processing pipelines. This is of special importance in clinical studies, reporting perfusion across ROIs defined on relatively undistorted images and when conducting group analyses requiring the alignment of images across different subjects.
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Affiliation(s)
- Catarina Domingos
- Institute for Systems and Robotics - Lisboa and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação, Funchal, Portugal.
| | - Ana R Fouto
- Institute for Systems and Robotics - Lisboa and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Rita G Nunes
- Institute for Systems and Robotics - Lisboa and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Amparo Ruiz-Tagle
- Institute for Systems and Robotics - Lisboa and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Inês Esteves
- Institute for Systems and Robotics - Lisboa and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | | | - Pedro Vilela
- Neurology Department, Hospital da Luz, Lisbon, Portugal
| | - Raquel Gil-Gouveia
- Neurology Department, Hospital da Luz, Lisbon, Portugal.; Center for Interdisciplinary Research in Health, Universidade Católica Portuguesa, Lisbon, Portugal
| | - Patrícia Figueiredo
- Institute for Systems and Robotics - Lisboa and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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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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7
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Garcia-Garcia B, Mattern H, Vockert N, Yakupov R, Schreiber F, Spallazzi M, Perosa V, Haghikia A, Speck O, Düzel E, Maass A, Schreiber S. Vessel Distance Mapping: A novel methodology for assessing vascular-induced cognitive resilience. Neuroimage 2023; 274:120094. [PMID: 37028734 DOI: 10.1016/j.neuroimage.2023.120094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023] Open
Abstract
The association between cerebral blood supply and cognition has been widely discussed in the recent literature. One focus of this discussion has been the anatomical variability of the circle of Willis, with morphological differences being present in more than half of the general population. While previous studies have attempted to classify these differences and explore their contribution to hippocampal blood supply and cognition, results have been controversial. To disentangle these previously inconsistent findings, we introduce Vessel Distance Mapping (VDM) as a novel methodology for evaluating blood supply, which allows for obtaining vessel pattern metrics with respect to the surrounding structures, extending the previously established binary classification into a continuous spectrum. To accomplish this, we manually segmented hippocampal vessels obtained from high-resolution 7T time-of-flight MR angiographic imaging in older adults with and without cerebral small vessel disease, generating vessel distance maps by computing the distances of each voxel to its nearest vessel. Greater values of VDM-metrics, which reflected higher vessel distances, were associated with poorer cognitive outcomes in subjects affected by vascular pathology, while this relation was not observed in healthy controls. Therefore, a mixed contribution of vessel pattern and vessel density is proposed to confer cognitive resilience, consistent with previous research findings. In conclusion, VDM provides a novel platform, based on a statistically robust and quantitative method of vascular mapping, for addressing a variety of clinical research questions.
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Affiliation(s)
| | - Hendrik Mattern
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Biomedical Magnetic Resonance, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany
| | - Niklas Vockert
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany
| | - Renat Yakupov
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Frank Schreiber
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Department of Neurology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Marco Spallazzi
- Department of Medicine and Surgery, Unit of Neurology, Azienda Ospedalierouniversitaria, 43126 Parma, Italy
| | - Valentina Perosa
- Department of Neurology, Otto-von-Guericke University, 39120, Magdeburg, Germany; J. Philip Kistler Stroke Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aiden Haghikia
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany; Department of Neurology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Oliver Speck
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Biomedical Magnetic Resonance, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany; Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Emrah Düzel
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany; Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, 39120 Magdeburg, Germany; Department of Neurology, Otto-von-Guericke University, 39120, Magdeburg, Germany; Institute of Cognitive Neuroscience, University College London, London WCIN 3AZ, UK
| | - Anne Maass
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany
| | - Stefanie Schreiber
- German Center for Neurodegenerative Diseases, 39120 Magdeburg, Germany; Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany; Department of Neurology, Otto-von-Guericke University, 39120, Magdeburg, Germany
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8
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Pfaffenrot V, Koopmans PJ. Magnetization transfer weighted laminar fMRI with multi-echo FLASH. Neuroimage 2022; 264:119725. [PMID: 36328273 DOI: 10.1016/j.neuroimage.2022.119725] [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: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Laminar functional magnetic resonance imaging (fMRI) using the gradient echo (GRE) blood oxygenation level dependent (BOLD) contrast is prone to signal changes arising from large unspecific venous vessels. Alternatives based on changes of cerebral blood volume (CBV) become more popular since it is expected that this hemodynamic response is dominant in microvasculature. One approach to sensitize the signal toward changes in CBV, and to simultaneously reduce unwanted extravascular (EV) BOLD blurring, is to selectively reduce gray matter (GM) signal via magnetization transfer (MT). In this work, we use off-resonant MT-pulses with a 3D FLASH readout to perform MT-prepared (MT-prep) laminar fMRI of the primary visual cortex (V1) at multiple echo times at 7 T. With a GRE-BOLD contrast without additional MT-weighting as reference, we investigated the influence of the MT-preparation on the shape and the echo time dependency of laminar profiles. Through numerical simulations, we optimized the sequence parameters to increase the sensitivity toward signal changes induced by changes in arterial CBV and to delineate the contributions of different compartments to the signal. We show that at 7 T, GM signals can be reduced by 30 %. Our laminar fMRI responses exhibit an increased signal change in the parenchyma at very short TE compared to a BOLD-only reference as a result of reduced EV signal intensity. By varying echo times, we could show that MT-prep results in less sensitivity toward unwanted signal changes based on changes in T2*. We conclude that when accounting for nuclear overhauser enhancement effects in blood, off-resonant MT-prep combined with efficient short TE readouts can become a promising method to reduce unwanted EV venous contributions in GRE-BOLD and/or to allow scanning at much shorter echo times without incurring a sensitivity penalty in laminar fMRI.
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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.
| | - 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; Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
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9
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Haarsma J, Kok P, Browning M. The promise of layer-specific neuroimaging for testing predictive coding theories of psychosis. Schizophr Res 2022; 245:68-76. [PMID: 33199171 PMCID: PMC9241988 DOI: 10.1016/j.schres.2020.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/03/2020] [Accepted: 10/28/2020] [Indexed: 12/24/2022]
Abstract
Predictive coding potentially provides an explanatory model for understanding the neurocognitive mechanisms of psychosis. It proposes that cognitive processes, such as perception and inference, are implemented by a hierarchical system, with the influence of each level being a function of the estimated precision of beliefs at that level. However, predictive coding models of psychosis are insufficiently constrained-any phenomenon can be explained in multiple ways by postulating different changes to precision at different levels of processing. One reason for the lack of constraint in these models is that the core processes are thought to be implemented by the function of specific cortical layers, and the technology to measure layer specific neural activity in humans has until recently been lacking. As a result, our ability to constrain the models with empirical data has been limited. In this review we provide a brief overview of predictive processing models of psychosis and then describe the potential for newly developed, layer specific neuroimaging techniques to test and thus constrain these models. We conclude by discussing the most promising avenues for this research as well as the technical and conceptual challenges which may limit its application.
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Affiliation(s)
- J. Haarsma
- Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom,Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Corresponding author at: Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom.
| | - P. Kok
- Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom
| | - M. Browning
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Oxford Health NHS Trust, Oxford, United Kingdom
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10
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Vizioli L, Yacoub E, Lewis LD. How pushing the spatiotemporal resolution of fMRI can advance neuroscience. Prog Neurobiol 2021; 207:102184. [PMID: 34767874 DOI: 10.1016/j.pneurobio.2021.102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Luca Vizioli
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN 55455, United States; Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, United States.
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN 55455, United States
| | - Laura D Lewis
- Department of Biomedical Engineering, Boston University, Boston, MA United States; Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA United States
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11
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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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12
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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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13
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Perceived and mentally rotated contents are differentially represented in cortical depth of V1. Commun Biol 2021; 4:1069. [PMID: 34521987 PMCID: PMC8440580 DOI: 10.1038/s42003-021-02582-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
Primary visual cortex (V1) in humans is known to represent both veridically perceived external input and internally-generated contents underlying imagery and mental rotation. However, it is unknown how the brain keeps these contents separate thus avoiding a mixture of the perceived and the imagined which could lead to potentially detrimental consequences. Inspired by neuroanatomical studies showing that feedforward and feedback connections in V1 terminate in different cortical layers, we hypothesized that this anatomical compartmentalization underlies functional segregation of external and internally-generated visual contents, respectively. We used high-resolution layer-specific fMRI to test this hypothesis in a mental rotation task. We found that rotated contents were predominant at outer cortical depth bins (i.e. superficial and deep). At the same time perceived contents were represented stronger at the middle cortical bin. These results identify how through cortical depth compartmentalization V1 functionally segregates rather than confuses external from internally-generated visual contents. These results indicate that feedforward and feedback manifest in distinct subdivisions of the early visual cortex, thereby reflecting a general strategy for implementing multiple cognitive functions within a single brain region. In order to test whether there is a cortical depth compartmentalization in the processing of external and internally-generated visual contents, Iamshchinina et al use high-resolution fMRI at 7 T in participants performing a mental rotation task. They demonstrate that feedforward and feedback representations during mental rotation manifest at differentiable grey matter depth in early visual cortex, thereby reflecting a general strategy for implementing multiple cognitive functions within a single brain region.
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14
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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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15
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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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16
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Zooming-in on higher-level vision: High-resolution fMRI for understanding visual perception and awareness. Prog Neurobiol 2021; 207:101998. [PMID: 33497652 DOI: 10.1016/j.pneurobio.2021.101998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 11/11/2020] [Accepted: 01/16/2021] [Indexed: 12/24/2022]
Abstract
One of the central questions in visual neuroscience is how the sparse retinal signals leaving our eyes are transformed into a rich subjective visual experience of the world. Invasive physiology studies, which offers the highest spatial resolution, have revealed many facts about the processing of simple visual features like contrast, color, and orientation, focusing on the early visual areas. At the same time, standard human fMRI studies with comparably coarser spatial resolution have revealed more complex, functionally specialized, and category-selective responses in higher visual areas. Although the visual system is the best understood among the sensory modalities, these two areas of research remain largely segregated. High-resolution fMRI opens up a possibility for linking them. On the one hand, it allows studying how the higher-level visual functions affect the fine-scale activity in early visual areas. On the other hand, it allows discovering the fine-scale functional organization of higher visual areas and exploring their functional connectivity with visual areas lower in the hierarchy. In this review, I will discuss examples of successful work undertaken in these directions using high-resolution fMRI and discuss where this method could be applied in the future to advance our understanding of the complexity of higher-level visual processing.
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17
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Stanley OW, Kuurstra AB, Klassen LM, Menon RS, Gati JS. Effects of phase regression on high-resolution functional MRI of the primary visual cortex. Neuroimage 2020; 227:117631. [PMID: 33316391 DOI: 10.1016/j.neuroimage.2020.117631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
High-resolution functional MRI studies have become a powerful tool to non-invasively probe the sub-millimeter functional organization of the human cortex. Advances in MR hardware, imaging techniques and sophisticated post-processing methods have allowed high resolution fMRI to be used in both the clinical and academic neurosciences. However, consensus within the community regarding the use of gradient echo (GE) or spin echo (SE) based acquisition remains largely divided. On one hand, GE provides a high temporal signal-to-noise ratio (tSNR) technique sensitive to both the macro- and micro-vascular signal while SE based methods are more specific to microvasculature but suffer from lower tSNR and specific absorption rate limitations, especially at high field and with short repetition times. Fortunately, the phase of the GE-EPI signal is sensitive to vessel size and this provides a potential avenue to reduce the macrovascular weighting of the signal (phase regression, Menon 2002). In order to determine the efficacy of this technique at high-resolution, phase regression was applied to GE-EPI timeseries and compared to SE-EPI to determine if GE-EPI's specificity to the microvascular compartment improved. To do this, functional data was collected from seven subjects on a neuro-optimized 7 T system at 800 μm isotropic resolution with both GE-EPI and SE-EPI while observing an 8 Hz contrast reversing checkerboard. Phase data from the GE-EPI was used to create a microvasculature-weighted time series (GE-EPI-PR). Anatomical imaging (MP2RAGE) was also collected to allow for surface segmentation so that the functional results could be projected onto a surface. A multi-echo gradient echo sequence was collected and used to identify venous vasculature. The GE-EPI-PR surface activation maps showed a high qualitative similarity with SE-EPI and also produced laminar activity profiles similar to SE-EPI. When the GE-EPI and GE-EPI-PR distributions were compared to SE-EPI it was shown that GE-EPI-PR had similar distribution characteristics to SE-EPI (p < 0.05) across the top 60% of cortex. Furthermore, it was shown that GE-EPI-PR has a higher contrast-to-noise ratio (0.5 ± 0.2, mean ± std. dev. across layers) than SE-EPI (0.27 ± 0.07) demonstrating the technique has higher sensitivity than SE-EPI. Taken together this evidence suggests phase regression is a useful method in low SNR studies such as high-resolution fMRI.
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Affiliation(s)
- Olivia W Stanley
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada.
| | - Alan B Kuurstra
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada
| | - L Martyn Klassen
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Ravi S Menon
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Joseph S Gati
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
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18
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Pérez-Rodas M, Pohmann R, Scheffler K, Heule R. Intravascular BOLD signal characterization of balanced SSFP experiments in human blood at high to ultrahigh fields. Magn Reson Med 2020; 85:2055-2068. [PMID: 33140871 DOI: 10.1002/mrm.28575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To investigate the intravascular contribution to the overall balanced SSFP (bSSFP) BOLD effect in human blood at high to ultrahigh field strengths (3 T, 9.4 T, and 14.1 T). METHODS Venous blood prepared at two different oxygenation levels (deoxygenated: Y ≈ 71%, oxygenated: Y ≈ 94%) was measured with phase-cycled bSSFP for varying TRs/flip angles at 3 T, 9.4 T, and 14.1 T. The oxygen sensitivity was analyzed by intrinsic MIRACLE (motion-insensitive rapid configuration relaxometry)-R2 estimation and passband signal differences. The intravascular BOLD-related signal change was extracted from the measured data for microvasculature and macrovasculature, and compared with the extravascular contribution obtained by Monte Carlo simulations. RESULTS The MIRACLE-R2 values showed a characteristic increase with longer TRs in deoxygenated blood, corroborating that SE-R2 data cannot be used to assess the intravascular bSSFP BOLD effect. Passband bSSFP signal differences measured at optimal flip angles of 30° at 3 T and 20° at 9.4 T/14.1 T revealed considerable relative intravascular contributions of 95%/70% at 3 T, 74%/43% at 9.4 T, 66%/46% at 14.1 T for TR = 5 ms, and 90%/65% at 3 T, 36%/27% at 9.4 T, 13%/15% at 14.1 T for TR = 10 ms in macrovascular/microvascular regimes. CONCLUSION The results indicate that intravascular effects have to be considered to better understand the origin of bSSFP BOLD contrast in functional MRI experiments, especially at short TRs. The MIRACLE-R2 method demonstrated the ability to quantify the apparent decrease in R2 due to rapid RF refocusing.
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Affiliation(s)
- Marlon Pérez-Rodas
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Graduate Training Centre of Neuroscience, IMPRS for Cognitive and Systems Neuroscience, University of Tübingen, Tübingen, Germany
| | - Rolf Pohmann
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Klaus Scheffler
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
| | - Rahel Heule
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Department of Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
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19
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Eye-selective fMRI activity in human primary visual cortex: Comparison between 3 T and 9.4 T, and effects across cortical depth. Neuroimage 2020; 220:117078. [DOI: 10.1016/j.neuroimage.2020.117078] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
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20
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Wallace TE, Polimeni JR, Stockmann JP, Hoge WS, Kober T, Warfield SK, Afacan O. Dynamic distortion correction for functional MRI using FID navigators. Magn Reson Med 2020; 85:1294-1307. [PMID: 32970869 DOI: 10.1002/mrm.28505] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To develop a method for slice-wise dynamic distortion correction for EPI using rapid spatiotemporal B0 field measurements from FID navigators (FIDnavs) and to evaluate the efficacy of this new approach relative to an established data-driven technique. METHODS A low-resolution reference image was used to create a forward model of FIDnav signal changes to enable estimation of spatiotemporal B0 inhomogeneity variations up to second order from measured FIDnavs. Five volunteers were scanned at 3 T using a 64-channel coil with FID-navigated EPI. The accuracy of voxel shift measurements and geometric distortion correction was assessed for experimentally induced magnetic field perturbations. The temporal SNR was evaluated in EPI time-series acquired at rest and with a continuous nose-touching action, before and after image realignment. RESULTS Field inhomogeneity coefficients and voxel shift maps measured using FIDnavs were in excellent agreement with multi-echo EPI measurements. The FID-navigated distortion correction accurately corrected image geometry in the presence of induced magnetic field perturbations, outperforming the data-driven approach in regions with large field offsets. In functional MRI scans with nose touching, FIDnav-based correction yielded temporal SNR gains of 30% in gray matter. Following image realignment, which accounted for global image shifts, temporal SNR gains of 3% were achieved. CONCLUSIONS Our proposed application of FIDnavs enables slice-wise dynamic distortion correction with high temporal efficiency. We achieved improved signal stability by leveraging the encoding information from multichannel coils. This approach can be easily adapted to other EPI-based sequences to improve temporal SNR for a variety of clinical and research applications.
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Affiliation(s)
- Tess E Wallace
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan R Polimeni
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jason P Stockmann
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - W Scott Hoge
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tobias Kober
- Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland.,Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,LTS5, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon K Warfield
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Onur Afacan
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
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21
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Bazin PL, Nijsse HE, van der Zwaag W, Gallichan D, Alkemade A, Vos FM, Forstmann BU, Caan MWA. Sharpness in motion corrected quantitative imaging at 7T. Neuroimage 2020; 222:117227. [PMID: 32781231 DOI: 10.1016/j.neuroimage.2020.117227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/03/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
Sub-millimeter imaging at 7T has opened new possibilities for qualitatively and quantitatively studying brain structure as it evolves throughout the life span. However, subject motion introduces image blurring on the order of magnitude of the spatial resolution and is thus detrimental to image quality. Such motion can be corrected for, but widespread application has not yet been achieved and quantitative evaluation is lacking. This raises a need to quantitatively measure image sharpness throughout the brain. We propose a method to quantify sharpness of brain structures at sub-voxel resolution, and use it to assess to what extent limited motion is related to image sharpness. The method was evaluated in a cohort of 24 healthy volunteers with a wide and uniform age range, aiming to arrive at results that largely generalize to larger populations. Using 3D fat-excited motion navigators, quantitative R1, R2* and Quantitative Susceptibility Maps and T1-weighted images were retrospectively corrected for motion. Sharpness was quantified in all modalities for selected regions of interest (ROI) by fitting the sigmoidally shaped error function to data within locally homogeneous clusters. A strong, almost linear correlation between motion and sharpness improvement was observed, and motion correction significantly improved sharpness. Overall, the Full Width at Half Maximum reduced from 0.88 mm to 0.70 mm after motion correction, equivalent to a 2.0 times smaller voxel volume. Motion and sharpness were not found to correlate with the age of study participants. We conclude that in our data, motion correction using fat navigators is overall able to restore the measured sharpness to the imaging resolution, irrespective of the amount of motion observed during scanning.
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Affiliation(s)
- Pierre-Louis Bazin
- Integrative Model-based Cognitive Neuroscience research unit, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands.
| | - Hannah E Nijsse
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands.
| | | | - Daniel Gallichan
- CUBRIC, School of Engineering, Cardiff University, Cardiff, United Kingdom.
| | - Anneke Alkemade
- Integrative Model-based Cognitive Neuroscience research unit, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands.
| | - Frans M Vos
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands.
| | - Birte U Forstmann
- Integrative Model-based Cognitive Neuroscience research unit, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands.
| | - Matthan W A Caan
- Amsterdam UMC, University of Amsterdam, Biomedical Engineering and Physics, Amsterdam, the Netherlands.
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