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Mishra A, Wang F, Chen LM, Gore JC. Machine Learning-Based Clustering of Layer-Resolved fMRI Activation and Functional Connectivity Within the Primary Somatosensory Cortex in Nonhuman Primates. Hum Brain Mapp 2025; 46:e70193. [PMID: 40095731 PMCID: PMC11912181 DOI: 10.1002/hbm.70193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 02/27/2025] [Accepted: 03/03/2025] [Indexed: 03/19/2025] Open
Abstract
Delineating the functional organization of mesoscale cortical columnar structure is essential for understanding brain function. We have previously demonstrated a high spatial correspondence between BOLD fMRI and LFP responses to tactile stimuli in the primary somatosensory cortex area 3b of nonhuman primates. This study aims to explore how 2D spatial profiles of the functional column vary across cortical layers (defined by three cortical depths) in both tactile stimulation and resting states using fMRI. At 9.4 T, we acquired submillimeter-resolution oblique fMRI data from cortical areas 3b and 1 of anesthetized squirrel monkeys and obtained fMRI signals from three cortical layers. In both areas 3b and 1, the tactile stimulus-evoked fMRI activation foci were fitted with point spread functions (PSFs), from which shape parameters, including full width at half maximum (FWHM), were derived. Seed-based resting-state fMRI data analysis was then performed to measure the spatial profiles of resting-state connectivity within and between areas 3b and 1. We found that the tactile-evoked fMRI response and local resting-state functional connectivity were elongated at the superficial layer, with the major axes oriented in lateral to medial (from digit 1 to digit 5) direction. This elongation was significantly reduced in the deeper (middle and bottom) layers. To assess the robustness of these spatial profiles in distinguishing cortical layers, shape parameters describing the spatial extents of activation and resting-state connectivity profiles were used to classify the layers via self-organizing maps (SOM). A minimal overall classification error (~13%) was achieved, effectively classifying the layers into two groups: the superficial layer exhibited distinct features from the two deeper layers in the rsfMRI data. Our results support distinct 2D spatial profiles for superficial versus deeper cortical layers and reveal similarities between stimulus-evoked and resting-state configurations.
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Affiliation(s)
- Arabinda Mishra
- Institute of Imaging ScienceVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Feng Wang
- Institute of Imaging ScienceVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Li Min Chen
- Institute of Imaging ScienceVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - John C. Gore
- Institute of Imaging ScienceVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical EngineeringVanderbilt UniversityNashvilleTennesseeUSA
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Yang Z, Arabinda M, Wang F, Chen LM, Gore JC. Layer-specific BOLD effects in gradient and spin-echo acquisitions in somatosensory cortex. Magn Reson Med 2025; 93:1314-1328. [PMID: 39370926 PMCID: PMC11680728 DOI: 10.1002/mrm.30326] [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: 07/17/2024] [Revised: 09/10/2024] [Accepted: 09/14/2024] [Indexed: 10/08/2024]
Abstract
PURPOSE Previous studies have shown varied BOLD signals with gradient echo (GE) across cortical depth. To interpret these variations, and understand the effects of vascular geometry and size, the magnitudes and layer distributions of GE and spin-echo (SE) BOLD functional MRI signals were compared in the somatosensory cortex of squirrel monkeys during tactile stimulation and in a resting state at high spatial resolution and high field. METHODS A block-design stimulation was used to identify tactile-evoked activation signals in somatosensory Areas 3b and 1. Layer-specific connectivities were calculated using resting-state data. Signal power spectra were compared by depth and pulse sequence. The measured ratios of transverse relaxation rate changes were compared with Anderson and Weiss's model. RESULTS SE signals showed a 26% lower percentage signal change during tactile stimulation compared with GE, along with a slower time course. SE signals remained consistent but weaker in lower layers, whereas GE signals decreased with cortical depth. This pattern extended to resting-state power spectra. Resting-state functional connectivity indicated larger connectivity between the top layers of Area 3b and Area 1 for GE, with minimal changes for SE. Comparisons with theory suggest vessel diameters ranging from 19.4 to 9 microns are responsible for BOLD effects across cortical layers at 9.4 T. CONCLUSION These results provide further evidence that at high field, SE BOLD signals are relatively free of contributions from sources other than microvascular changes in response to neural activity, whereas GE signals, even in the superficial layers, are not dominated by very large vessels.
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Affiliation(s)
- Zhangyan Yang
- Institute of Imaging ScienceVanderbilt University Medical Center
NashvilleTennesseeUSA
- Department of Biomedical EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Mishra Arabinda
- Institute of Imaging ScienceVanderbilt University Medical Center
NashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Feng Wang
- Institute of Imaging ScienceVanderbilt University Medical Center
NashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Li Min Chen
- Institute of Imaging ScienceVanderbilt University Medical Center
NashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - John C. Gore
- Institute of Imaging ScienceVanderbilt University Medical Center
NashvilleTennesseeUSA
- Department of Biomedical EngineeringVanderbilt UniversityNashvilleTennesseeUSA
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Physics and AstronomyVanderbilt UniversityNashvilleTennesseeUSA
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Hikishima K, Tsurugizawa T, Kasahara K, Takagi R, Yoshinaka K, Nitta N. Brain-wide mapping of resting-state networks in mice using high-frame rate functional ultrasound. Neuroimage 2023; 279:120297. [PMID: 37500027 DOI: 10.1016/j.neuroimage.2023.120297] [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: 04/21/2023] [Revised: 06/21/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Functional ultrasound (fUS) imaging is a method for visualizing deep brain activity based on cerebral blood volume changes coupled with neural activity, while functional MRI (fMRI) relies on the blood-oxygenation-level-dependent signal coupled with neural activity. Low-frequency fluctuations (LFF) of fMRI signals during resting-state can be measured by resting-state fMRI (rsfMRI), which allows functional imaging of the whole brain, and the distributions of resting-state network (RSN) can then be estimated from these fluctuations using independent component analysis (ICA). This procedure provides an important method for studying cognitive and psychophysiological diseases affecting specific brain networks. The distributions of RSNs in the brain-wide area has been reported primarily by rsfMRI. RSNs using rsfMRI are generally computed from the time-course of fMRI signals for more than 5 min. However, a recent dynamic functional connectivity study revealed that RSNs are still not perfectly stable even after 10 min. Importantly, fUS has a higher temporal resolution and stronger correlation with neural activity compared with fMRI. Therefore, we hypothesized that fUS applied during the resting-state for a shorter than 5 min would provide similar RSNs compared to fMRI. High temporal resolution rsfUS data were acquired at 10 Hz in awake mice. The quality of the default mode network (DMN), a well-known RSN, was evaluated using signal-noise separation (SNS) applied to different measurement durations of rsfUS. The results showed that the SNS did not change when the measurement duration was increased to more than 210 s. Next, we measured short-duration rsfUS multi-slice measurements in the brain-wide area. The results showed that rsfUS with the short duration succeeded in detecting RSNs distributed in the brain-wide area consistent with RSNs detected by 11.7-T MRI under awake conditions (medial prefrontal cortex and cingulate cortex in the anterior DMN, retrosplenial cortex and visual cortex in the posterior DMN, somatosensory and motor cortexes in the lateral cortical network, thalamus, dorsal hippocampus, and medial cerebellum), confirming the reliability of the RSNs detected by rsfUS. However, bilateral RSNs located in the secondary somatosensory cortex, ventral hippocampus, auditory cortex, and lateral cerebellum extracted from rsfUS were different from the unilateral RSNs extracted from rsfMRI. These findings indicate the potential of rsfUS as a method for analyzing functional brain networks and should encourage future research to elucidate functional brain networks and their relationships with disease model mice.
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Affiliation(s)
- Keigo Hikishima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan; Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan.
| | - Tomokazu Tsurugizawa
- Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Kazumi Kasahara
- Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Ryo Takagi
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Kiyoshi Yoshinaka
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Naotaka Nitta
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
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Liu ZQ, Shafiei G, Baillet S, Misic B. Spatially heterogeneous structure-function coupling in haemodynamic and electromagnetic brain networks. Neuroimage 2023; 278:120276. [PMID: 37451374 DOI: 10.1016/j.neuroimage.2023.120276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
The relationship between structural and functional connectivity in the brain is a key question in connectomics. Here we quantify patterns of structure-function coupling across the neocortex, by comparing structural connectivity estimated using diffusion MRI with functional connectivity estimated using both neurophysiological (MEG-based) and haemodynamic (fMRI-based) recordings. We find that structure-function coupling is heterogeneous across brain regions and frequency bands. The link between structural and functional connectivity is generally stronger in multiple MEG frequency bands compared to resting state fMRI. Structure-function coupling is greater in slower and intermediate frequency bands compared to faster frequency bands. We also find that structure-function coupling systematically follows the archetypal sensorimotor-association hierarchy, as well as patterns of laminar differentiation, peaking in granular layer IV. Finally, structure-function coupling is better explained using structure-informed inter-regional communication metrics than using structural connectivity alone. Collectively, these results place neurophysiological and haemodynamic structure-function relationships in a common frame of reference and provide a starting point for a multi-modal understanding of structure-function coupling in the brain.
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Affiliation(s)
- Zhen-Qi Liu
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Golia Shafiei
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sylvain Baillet
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada.
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Carlson BM, Mitchell BA, Dougherty K, Westerberg JA, Cox MA, Maier A. Does V1 response suppression initiate binocular rivalry? iScience 2023; 26:107359. [PMID: 37520732 PMCID: PMC10382945 DOI: 10.1016/j.isci.2023.107359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
During binocular rivalry (BR) only one eye's view is perceived. Neural underpinnings of BR are debated. Recent studies suggest that primary visual cortex (V1) initiates BR. One trigger might be response suppression across most V1 neurons at the onset of BR. Here, we utilize a variant of BR called binocular rivalry flash suppression (BRFS) to test this hypothesis. BRFS is identical to BR, except stimuli are shown with a ∼1s delay. If V1 response suppression was required to initiate BR, it should occur during BRFS as well. To test this, we compared V1 spiking in two macaques observing BRFS. We found that BRFS resulted in response facilitation rather than response suppression across V1 neurons. However, BRFS still reduces responses in a subset of V1 neurons due to the adaptive effects of asynchronous stimulus presentation. We argue that this selective response suppression could serve as an alternate initiator of BR.
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Affiliation(s)
- Brock M. Carlson
- Department of Psychology, College of Arts and Science, Vanderbilt Vision Research Center, Center for Integrative and Cognitive Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
| | - Blake A. Mitchell
- Department of Psychology, College of Arts and Science, Vanderbilt Vision Research Center, Center for Integrative and Cognitive Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
| | - Kacie Dougherty
- Department of Psychology, College of Arts and Science, Vanderbilt Vision Research Center, Center for Integrative and Cognitive Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
- Department of Psychology, Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08540, USA
| | - Jacob A. Westerberg
- Department of Psychology, College of Arts and Science, Vanderbilt Vision Research Center, Center for Integrative and Cognitive Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
- Department of Vision and Cognition, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam 1105 BA, the Netherlands
| | - Michele A. Cox
- Department of Psychology, College of Arts and Science, Vanderbilt Vision Research Center, Center for Integrative and Cognitive Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
- Center for Visual Science, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Maier
- Department of Psychology, College of Arts and Science, Vanderbilt Vision Research Center, Center for Integrative and Cognitive Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
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Qu S, Shi S, Quan Z, Gao Y, Wang M, Wang Y, Pan G, Lai HY, Roe AW, Zhang X. Design and application of a multimodality-compatible 1Tx/6Rx RF coil for monkey brain MRI at 7T. Neuroimage 2023; 276:120185. [PMID: 37244320 DOI: 10.1016/j.neuroimage.2023.120185] [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: 04/11/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVE Blood-oxygen-level-dependent functional MRI allows to investigte neural activities and connectivity. While the non-human primate plays an essential role in neuroscience research, multimodal methods combining functional MRI with other neuroimaging and neuromodulation enable us to understand the brain network at multiple scales. APPROACH In this study, a tight-fitting helmet-shape receive array with a single transmit loop for anesthetized macaque brain MRI at 7T was fabricated with four openings constructed in the coil housing to accommodate multimodal devices, and the coil performance was quantitatively evaluated and compared to a commercial knee coil. In addition, experiments over three macaques with infrared neural stimulation (INS), focused ultrasound stimulation (FUS), and transcranial direct current stimulation (tDCS) were conducted. MAIN RESULTS The RF coil showed higher transmit efficiency, comparable homogeneity, improved SNR and enlarged signal coverage over the macaque brain. Infrared neural stimulation was applied to the amygdala in deep brain region, and activations in stimulation sites and connected sites were detected, with the connectivity consistent with anatomical information. Focused ultrasound stimulation was applied to the left visual cortex, and activations were acquired along the ultrasound traveling path, with all time course curves consistent with pre-designed paradigms. The existence of transcranial direct current stimulation electrodes brought no interference to the RF system, as evidenced through high-resolution MPRAGE structure images. SIGNIFICANCE This pilot study reveals the feasibility for brain investigation at multiple spatiotemporal scales, which may advance our understanding in dynamic brain networks.
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Affiliation(s)
- Shuxian Qu
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China
| | - Sunhang Shi
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China
| | - Zhiyan Quan
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China
| | - Yang Gao
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China; College of Electrical Engineering, Zhejiang University, Hangzhou, China
| | - Minmin Wang
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, China
| | - Yueming Wang
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, China; State Key Lab of CAD&CG, Zhejiang University, Hangzhou, China
| | - Gang Pan
- MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China; State Key Lab of CAD&CG, Zhejiang University, Hangzhou, China.
| | - Hsin-Yi Lai
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China; Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
| | - Anna Wang Roe
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China; Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaotong Zhang
- The Interdisciplinary Institute of Neuroscience and Technology, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou, China; Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China; College of Electrical Engineering, Zhejiang University, Hangzhou, China.
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MacDonald D, van Veggel FCJM, Tomanek B, Blasiak B. Contrast Enhancement in MRI Using Combined Double Action Contrast Agents and Image Post-Processing in the Breast Cancer Model. MATERIALS (BASEL, SWITZERLAND) 2023; 16:3096. [PMID: 37109931 PMCID: PMC10142138 DOI: 10.3390/ma16083096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Gd- and Fe-based contrast agents reduce T1 and T2 relaxation times, respectively, are frequently used in MRI, providing improved cancer detection. Recently, contrast agents changing both T1/T2 times, based on core/shell nanoparticles, have been introduced. Although advantages of the T1/T2 agents were shown, MR image contrast of cancerous versus normal adjacent tissue induced by these agents has not yet been analyzed in detail as authors considered changes in cancer MR signal or signal-to-noise ratio after contrast injection rather than changes in signal differences between cancer and normal adjacent tissue. Furthermore, the potential advantages of T1/T2 contrast agents using image manipulation such as subtraction or addition have not been yet discussed in detail. Therefore, we performed theoretical calculations of MR signal in a tumor model using T1-weighted, T2-weighted, and combined images for T1-, T2-, and T1/T2-targeted contrast agents. The results from the tumor model are followed by in vivo experiments using core/shell NaDyF4/NaGdF4 nanoparticles as T1/T2 non-targeted contrast agent in the animal model of triple negative breast cancer. The results show that subtraction of T2-weighted from T1-weighted MR images provides additional increase in the tumor contrast: over two-fold in the tumor model and 12% in the in vivo experiment.
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Affiliation(s)
- David MacDonald
- Institute of Nuclear Physics Polish Academy of Science, Radzikowskiego 152, 31-342 Krakow, Poland; (D.M.); (B.T.)
| | - Frank C. J. M. van Veggel
- Department of Chemistry, Centre for Advanced Materials & Related Technologies (CAMTEC), University of Victoria, Victoria, BC V8P 5C2, Canada;
| | - Boguslaw Tomanek
- Institute of Nuclear Physics Polish Academy of Science, Radzikowskiego 152, 31-342 Krakow, Poland; (D.M.); (B.T.)
- Division of Medical Physics, Department of Oncology, University of Alberta, 8303 112 St NW, Edmonton, AB T6G 2T4, Canada
- Department of Clinical Neurosciences and Radiology, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Barbara Blasiak
- Institute of Nuclear Physics Polish Academy of Science, Radzikowskiego 152, 31-342 Krakow, Poland; (D.M.); (B.T.)
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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: 2.0] [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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Shafiei G, Baillet S, Misic B. Human electromagnetic and haemodynamic networks systematically converge in unimodal cortex and diverge in transmodal cortex. PLoS Biol 2022; 20:e3001735. [PMID: 35914002 PMCID: PMC9371256 DOI: 10.1371/journal.pbio.3001735] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 08/11/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022] Open
Abstract
Whole-brain neural communication is typically estimated from statistical associations among electromagnetic or haemodynamic time-series. The relationship between functional network architectures recovered from these 2 types of neural activity remains unknown. Here, we map electromagnetic networks (measured using magnetoencephalography (MEG)) to haemodynamic networks (measured using functional magnetic resonance imaging (fMRI)). We find that the relationship between the 2 modalities is regionally heterogeneous and systematically follows the cortical hierarchy, with close correspondence in unimodal cortex and poor correspondence in transmodal cortex. Comparison with the BigBrain histological atlas reveals that electromagnetic-haemodynamic coupling is driven by laminar differentiation and neuron density, suggesting that the mapping between the 2 modalities can be explained by cytoarchitectural variation. Importantly, haemodynamic connectivity cannot be explained by electromagnetic activity in a single frequency band, but rather arises from the mixing of multiple neurophysiological rhythms. Correspondence between the two is largely driven by MEG functional connectivity at the beta (15 to 29 Hz) frequency band. Collectively, these findings demonstrate highly organized but only partly overlapping patterns of connectivity in MEG and fMRI functional networks, opening fundamentally new avenues for studying the relationship between cortical microarchitecture and multimodal connectivity patterns.
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Affiliation(s)
- Golia Shafiei
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Sylvain Baillet
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
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Moerel M, Yacoub E, Gulban OF, Lage-Castellanos A, De Martino F. Using high spatial resolution fMRI to understand representation in the auditory network. Prog Neurobiol 2021; 207:101887. [PMID: 32745500 PMCID: PMC7854960 DOI: 10.1016/j.pneurobio.2020.101887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/27/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Following rapid methodological advances, ultra-high field (UHF) functional and anatomical magnetic resonance imaging (MRI) has been repeatedly and successfully used for the investigation of the human auditory system in recent years. Here, we review this work and argue that UHF MRI is uniquely suited to shed light on how sounds are represented throughout the network of auditory brain regions. That is, the provided gain in spatial resolution at UHF can be used to study the functional role of the small subcortical auditory processing stages and details of cortical processing. Further, by combining high spatial resolution with the versatility of MRI contrasts, UHF MRI has the potential to localize the primary auditory cortex in individual hemispheres. This is a prerequisite to study how sound representation in higher-level auditory cortex evolves from that in early (primary) auditory cortex. Finally, the access to independent signals across auditory cortical depths, as afforded by UHF, may reveal the computations that underlie the emergence of an abstract, categorical sound representation based on low-level acoustic feature processing. Efforts on these research topics are underway. Here we discuss promises as well as challenges that come with studying these research questions using UHF MRI, and provide a future outlook.
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Affiliation(s)
- Michelle Moerel
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, the Netherlands; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, the Netherlands.
| | - Essa Yacoub
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA.
| | - Omer Faruk Gulban
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, the Netherlands; Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Brain Innovation B.V., Maastricht, the Netherlands.
| | - Agustin Lage-Castellanos
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, the Netherlands; Department of NeuroInformatics, Cuban Center for Neuroscience, Cuba.
| | - Federico De Martino
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, the Netherlands; Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA.
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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: 1.5] [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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12
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One-pot synthesis of carboxymethyl-dextran coated iron oxide nanoparticles (CION) for preclinical fMRI and MRA applications. Neuroimage 2021; 238:118213. [PMID: 34116153 PMCID: PMC8418149 DOI: 10.1016/j.neuroimage.2021.118213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/15/2021] [Accepted: 05/25/2021] [Indexed: 11/21/2022] Open
Abstract
Superparamagnetic iron-oxide nanoparticles are robust contrast agents for magnetic resonance imaging (MRI) used for sensitive structural and functional mapping of the cerebral blood volume (CBV) when administered intravenously. To date, many CBV-MRI studies are conducted with Feraheme, manufactured for the clinical treatment of iron-deficiency. Unfortunately, Feraheme is currently not available outside the United States due to commercial and regulatory constraints, making CBV-MRI methods either inaccessible or very costly to achieve. To address this barrier, we developed a simple, one-pot recipe to synthesize Carboxymethyl-dextran coated Iron Oxide Nanoparticles, namely, “CION”, suitable for preclinical CBV-MRI applications. Here we disseminate a step-by-step instruction of our one-pot synthesis protocol, which allows CION to be produced in laboratories with minimal cost. We also characterized different CION-conjugations by manipulating polymer to metal stoichiometric ratio in terms of their size, surface chemistry, and chemical composition, and shifts in MR relaxivity and pharmacokinetics. We performed several proof-of-concept experiments in vivo, demonstrating the utility of CION for functional and structural MRI applications, including hypercapnic CO2 challenge, visual stimulation, targeted optogenetic stimulation, and microangiography. We also present evidence that CION can serve as a cross-modality research platform by showing concurrent in vivo optical and MRI measurement of CBV using fluorescent-labeled CION. The simplicity and cost-effectiveness of our one-pot synthesis method should allow researchers to reproduce CION and tailor the relaxivity and pharmacokinetics according to their imaging needs. It is our hope that this work makes CBV-MRI more openly available and affordable for a variety of research applications.
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13
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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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14
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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: 24] [Impact Index Per Article: 6.0] [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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15
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van Dijk JA, Fracasso A, Petridou N, Dumoulin SO. Validating Linear Systems Analysis for Laminar fMRI: Temporal Additivity for Stimulus Duration Manipulations. Brain Topogr 2021; 34:88-101. [PMID: 33210193 PMCID: PMC7803719 DOI: 10.1007/s10548-020-00808-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/05/2020] [Indexed: 11/26/2022]
Abstract
Advancements in ultra-high field (7 T and higher) magnetic resonance imaging (MRI) scanners have made it possible to investigate both the structure and function of the human brain at a sub-millimeter scale. As neuronal feedforward and feedback information arrives in different layers, sub-millimeter functional MRI has the potential to uncover information processing between cortical micro-circuits across cortical depth, i.e. laminar fMRI. For nearly all conventional fMRI analyses, the main assumption is that the relationship between local neuronal activity and the blood oxygenation level dependent (BOLD) signal adheres to the principles of linear systems theory. For laminar fMRI, however, directional blood pooling across cortical depth stemming from the anatomy of the cortical vasculature, potentially violates these linear system assumptions, thereby complicating analysis and interpretation. Here we assess whether the temporal additivity requirement of linear systems theory holds for laminar fMRI. We measured responses elicited by viewing stimuli presented for different durations and evaluated how well the responses to shorter durations predicted those elicited by longer durations. We find that BOLD response predictions are consistently good predictors for observed responses, across all cortical depths, and in all measured visual field maps (V1, V2, and V3). Our results suggest that the temporal additivity assumption for linear systems theory holds for laminar fMRI. We thus show that the temporal additivity assumption holds across cortical depth for sub-millimeter gradient-echo BOLD fMRI in early visual cortex.
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Affiliation(s)
- Jelle A van Dijk
- Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands.
- Experimental Psychology, Utrecht University, Utrecht, The Netherlands.
| | - Alessio Fracasso
- Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands
- Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, G12 8QB, UK
- Radiology Department, Imaging Division, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Natalia Petridou
- Radiology Department, Imaging Division, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Serge O Dumoulin
- Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands
- Experimental Psychology, Utrecht University, Utrecht, The Netherlands
- Experimental and Applied Psychology, VU University, Amsterdam, The Netherlands
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16
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Berman AJL, Grissom WA, Witzel T, Nasr S, Park DJ, Setsompop K, Polimeni JR. Ultra-high spatial resolution BOLD fMRI in humans using combined segmented-accelerated VFA-FLEET with a recursive RF pulse design. Magn Reson Med 2020; 85:120-139. [PMID: 32705723 DOI: 10.1002/mrm.28415] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To alleviate the spatial encoding limitations of single-shot echo-planar imaging (EPI) by developing multi-shot segmented EPI for ultra-high-resolution functional MRI (fMRI) with reduced ghosting artifacts from subject motion and respiration. THEORY AND METHODS Segmented EPI can reduce readout duration and reduce acceleration factors, however, the time elapsed between segment acquisitions (on the order of seconds) can result in intermittent ghosting, limiting its use for fMRI. Here, "FLEET" segment ordering, where segments are looped over before slices, was combined with a variable flip angle progression (VFA-FLEET) to improve inter-segment fidelity and maximize signal for fMRI. Scaling a sinc pulse's flip angle for each segment (VFA-FLEET-Sinc) produced inconsistent slice profiles and ghosting, therefore, a recursive Shinnar-Le Roux (SLR) radiofrequency (RF) pulse design was developed (VFA-FLEET-SLR) to generate unique pulses for every segment that together produce consistent slice profiles and signals. RESULTS The temporal stability of VFA-FLEET-SLR was compared against conventional-segmented EPI and VFA-FLEET-Sinc at 3T and 7T. VFA-FLEET-SLR showed reductions in both intermittent and stable ghosting compared to conventional-segmented and VFA-FLEET-Sinc, resulting in improved image quality with a minor trade-off in temporal SNR. Combining VFA-FLEET-SLR with acceleration, we achieved a 0.6-mm isotropic acquisition at 7T, without zoomed imaging or partial Fourier, demonstrating reliable detection of blood oxygenation level-dependent (BOLD) responses to a visual stimulus. To counteract the increased repetition time from segmentation, simultaneous multi-slice VFA-FLEET-SLR was demonstrated using RF-encoded controlled aliasing. CONCLUSIONS VFA-FLEET with a recursive RF pulse design supports acquisitions with low levels of artifact and spatial blur, enabling fMRI at previously inaccessible spatial resolutions with a "full-brain" field of view.
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Affiliation(s)
- Avery J L Berman
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - William A Grissom
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Thomas Witzel
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shahin Nasr
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel J Park
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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17
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Han S, Liao C, Manhard MK, Park DJ, Bilgic B, Fair MJ, Wang F, Blazejewska AI, Grissom WA, Polimeni JR, Setsompop K. Accelerated spin-echo functional MRI using multisection excitation by simultaneous spin-echo interleaving (MESSI) with complex-encoded generalized slice dithered enhanced resolution (cgSlider) simultaneous multislice echo-planar imaging. Magn Reson Med 2020; 84:206-220. [PMID: 31840295 PMCID: PMC7083698 DOI: 10.1002/mrm.28108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Spin-echo functional MRI (SE-fMRI) has the potential to improve spatial specificity when compared with gradient-echo fMRI. However, high spatiotemporal resolution SE-fMRI with large slice-coverage is challenging as SE-fMRI requires a long echo time to generate blood oxygenation level-dependent (BOLD) contrast, leading to long repetition times. The aim of this work is to develop an acquisition method that enhances the slice-coverage of SE-fMRI at high spatiotemporal resolution. THEORY AND METHODS An acquisition scheme was developed entitled multisection excitation by simultaneous spin-echo interleaving (MESSI) with complex-encoded generalized slice dithered enhanced resolution (cgSlider). MESSI uses the dead-time during the long echo time by interleaving the excitation and readout of 2 slices to enable 2× slice-acceleration, while cgSlider uses the stable temporal background phase in SE-fMRI to encode/decode 2 adjacent slices simultaneously with a "phase-constrained" reconstruction method. The proposed cgSlider-MESSI was also combined with simultaneous multislice (SMS) to achieve further slice-acceleration. This combined approach was used to achieve 1.5-mm isotropic whole-brain SE-fMRI with a temporal resolution of 1.5 s and was evaluated using sensory stimulation and breath-hold tasks at 3T. RESULTS Compared with conventional SE-SMS, cgSlider-MESSI-SMS provides 4-fold increase in slice-coverage for the same repetition time, with comparable temporal signal-to-noise ratio. Corresponding fMRI activation from cgSlider-MESSI-SMS for both fMRI tasks were consistent with those from conventional SE-SMS. Overall, cgSlider-MESSI-SMS achieved a 32× encoding-acceleration by combining Rinplane × MB × cgSlider × MESSI = 4 × 2 × 2 × 2. CONCLUSION High-quality, high-resolution whole-brain SE-fMRI was acquired at a short repetition time using cgSlider-MESSI-SMS. This method should be beneficial for high spatiotemporal resolution SE-fMRI studies requiring whole-brain coverage.
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Affiliation(s)
- SoHyun Han
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Congyu Liao
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Mary Kate Manhard
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Daniel Joseph Park
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Merlin J. Fair
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
| | - Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Medical Engineering & Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts
| | - Anna I. Blazejewska
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
| | - William A. Grissom
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Jonathan R. Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Radiology, Harvard Medical School, Boston, Massachusetts
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts
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18
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Beckett AJS, Dadakova T, Townsend J, Huber L, Park S, Feinberg DA. Comparison of BOLD and CBV using 3D EPI and 3D GRASE for cortical layer functional MRI at 7 T. Magn Reson Med 2020; 84:3128-3145. [PMID: 32557752 DOI: 10.1002/mrm.28347] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 01/27/2023]
Abstract
PURPOSE Functional MRI (fMRI) at the mesoscale of cortical layers and columns requires both sensitivity and specificity, the latter of which can be compromised if the imaging method is affected by vascular artifacts, particularly cortical draining veins at the pial surface. Recent studies have shown that cerebral blood volume (CBV) imaging is more specific to the actual laminar locus of neural activity than BOLD imaging using standard gradient-echo EPI sequences. Gradient and spin-echo (GRASE) BOLD imaging has also shown greater specificity when compared with standard gradient-echo EPI BOLD. Here we directly compare CBV and BOLD contrasts in high-resolution imaging of the primary motor cortex for laminar functional MRI in four combinations of signal labeling, CBV using slice-selective slab-inversion vascular space occupancy (VASO) and BOLD, each with 3D gradient-echo EPI and zoomed 3D-GRASE image readouts. METHODS Activations were measured using each sequence and contrast combination during a motor task. Activation profiles across cortical depth were measured to assess the sensitivity and specificity (pial bias) of each method. RESULTS Both CBV imaging using gradient-echo 3D-EPI and BOLD imaging using 3D-GRASE show similar specificity and sensitivity and are therefore useful tools for mesoscopic functional MRI in the human cortex. The combination of GRASE and VASO did not demonstrate high levels of sensitivity, nor show increased specificity. CONCLUSION Three-dimensional EPI with VASO contrast and 3D-GRASE with BOLD contrast both demonstrate sufficient sensitivity and specificity for laminar functional MRI to be used by neuroscientists in a wide range of investigations of depth-dependent neural circuitry in the human brain.
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Affiliation(s)
- Alexander J S Beckett
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA.,Advanced MRI Technologies, Sebastopol, California, USA
| | - Tetiana Dadakova
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - Jennifer Townsend
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA.,Advanced MRI Technologies, Sebastopol, California, USA
| | - Laurentius Huber
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Suhyung Park
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA.,Advanced MRI Technologies, Sebastopol, California, USA
| | - David A Feinberg
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA.,Advanced MRI Technologies, Sebastopol, California, USA
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19
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van Dijk JA, Fracasso A, Petridou N, Dumoulin SO. Linear systems analysis for laminar fMRI: Evaluating BOLD amplitude scaling for luminance contrast manipulations. Sci Rep 2020; 10:5462. [PMID: 32214136 PMCID: PMC7096513 DOI: 10.1038/s41598-020-62165-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/09/2020] [Indexed: 01/18/2023] Open
Abstract
A fundamental assumption of nearly all functional magnetic resonance imaging (fMRI) analyses is that the relationship between local neuronal activity and the blood oxygenation level dependent (BOLD) signal can be described as following linear systems theory. With the advent of ultra-high field (7T and higher) MRI scanners, it has become possible to perform sub-millimeter resolution fMRI in humans. A novel and promising application of sub-millimeter fMRI is measuring responses across cortical depth, i.e. laminar imaging. However, the cortical vasculature and associated directional blood pooling towards the pial surface strongly influence the cortical depth-dependent BOLD signal, particularly for gradient-echo BOLD. This directional pooling may potentially affect BOLD linearity across cortical depth. Here we assess whether the amplitude scaling assumption for linear systems theory holds across cortical depth. For this, we use stimuli with different luminance contrasts to elicit different BOLD response amplitudes. We find that BOLD amplitude across cortical depth scales with luminance contrast, and that this scaling is identical across cortical depth. Although nonlinearities may be present for different stimulus configurations and acquisition protocols, our results suggest that the amplitude scaling assumption for linear systems theory across cortical depth holds for luminance contrast manipulations in sub-millimeter laminar BOLD fMRI.
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Affiliation(s)
- Jelle A van Dijk
- Experimental Psychology, Utrecht University, Utrecht, NL, Netherlands.
- Spinoza Centre for Neuroimaging, Amsterdam, NL, Netherlands.
| | - Alessio Fracasso
- Spinoza Centre for Neuroimaging, Amsterdam, NL, Netherlands
- Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, G12 8QB, UK
- Radiology Department, Imaging Division, Center for Image Sciences, University Medical Center Utrecht, Utrecht, NL, Netherlands
| | - Natalia Petridou
- Radiology Department, Imaging Division, Center for Image Sciences, University Medical Center Utrecht, Utrecht, NL, Netherlands
| | - Serge O Dumoulin
- Experimental Psychology, Utrecht University, Utrecht, NL, Netherlands
- Spinoza Centre for Neuroimaging, Amsterdam, NL, Netherlands
- Experimental and Applied Psychology, VU University, Amsterdam, NL, Netherlands
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20
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Gau R, Bazin PL, Trampel R, Turner R, Noppeney U. Resolving multisensory and attentional influences across cortical depth in sensory cortices. eLife 2020; 9:46856. [PMID: 31913119 PMCID: PMC6984812 DOI: 10.7554/elife.46856] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 01/07/2020] [Indexed: 11/13/2022] Open
Abstract
In our environment, our senses are bombarded with a myriad of signals, only a subset of which is relevant for our goals. Using sub-millimeter-resolution fMRI at 7T, we resolved BOLD-response and activation patterns across cortical depth in early sensory cortices to auditory, visual and audiovisual stimuli under auditory or visual attention. In visual cortices, auditory stimulation induced widespread inhibition irrespective of attention, whereas auditory relative to visual attention suppressed mainly central visual field representations. In auditory cortices, visual stimulation suppressed activations, but amplified responses to concurrent auditory stimuli, in a patchy topography. Critically, multisensory interactions in auditory cortices were stronger in deeper laminae, while attentional influences were greatest at the surface. These distinct depth-dependent profiles suggest that multisensory and attentional mechanisms regulate sensory processing via partly distinct circuitries. Our findings are crucial for understanding how the brain regulates information flow across senses to interact with our complex multisensory world.
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Affiliation(s)
- Remi Gau
- Computational Neuroscience and Cognitive Robotics Centre, University of Birmingham, Birmingham, United Kingdom.,Institute of Psychology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium.,Institute of Neuroscience, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre-Louis Bazin
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,Integrative Model-based Cognitive Neuroscience research unit, University of Amsterdam, Amsterdam, Netherlands
| | - Robert Trampel
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Robert Turner
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom
| | - Uta Noppeney
- Computational Neuroscience and Cognitive Robotics Centre, University of Birmingham, Birmingham, United Kingdom.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
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21
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Havlicek M, Uludağ K. A dynamical model of the laminar BOLD response. Neuroimage 2020; 204:116209. [DOI: 10.1016/j.neuroimage.2019.116209] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/11/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
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22
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Quintana DD, Lewis SE, Anantula Y, Garcia JA, Sarkar SN, Cavendish JZ, Brown CM, Simpkins JW. The cerebral angiome: High resolution MicroCT imaging of the whole brain cerebrovasculature in female and male mice. Neuroimage 2019; 202:116109. [PMID: 31446129 PMCID: PMC6942880 DOI: 10.1016/j.neuroimage.2019.116109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/15/2019] [Accepted: 08/17/2019] [Indexed: 01/09/2023] Open
Abstract
The cerebrovascular system provides crucial functions that maintain metabolic and homeostatic states of the brain. Despite its integral role of supporting cerebral viability, the topological organization of these networks remains largely uncharacterized. This void in our knowledge surmises entirely from current technological limitations that prevent the capturing of data through the entire depth of the brain. We report high-resolution reconstruction and analysis of the complete vascular network of the entire brain at the capillary level in adult female and male mice using a vascular corrosion cast procedure. Vascular network analysis of the whole brain revealed sex-related differences of vessel hierarchy. In addition, region-specific network analysis demonstrated different patterns of angioarchitecture between brain subregions and sex. Furthermore, our group is the first to provide a three-dimensional analysis of the angioarchitecture and network organization in a single reconstructed tomographic data set that encompasses all hierarchy of vessels in the brain of the adult mouse.
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Affiliation(s)
- D D Quintana
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - S E Lewis
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - Y Anantula
- Department of Neuroscience, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - J A Garcia
- Department of Neuroscience, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - S N Sarkar
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - J Z Cavendish
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - C M Brown
- Department of Neuroscience, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - J W Simpkins
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA.
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Non-BOLD contrast for laminar fMRI in humans: CBF, CBV, and CMRO2. Neuroimage 2019; 197:742-760. [DOI: 10.1016/j.neuroimage.2017.07.041] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/10/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
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24
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Strategies and prospects for cortical depth dependent T2 and T2* weighted BOLD fMRI studies. Neuroimage 2019; 197:668-676. [DOI: 10.1016/j.neuroimage.2019.03.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 02/28/2019] [Accepted: 03/12/2019] [Indexed: 12/15/2022] Open
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Turner R. Myelin and Modeling: Bootstrapping Cortical Microcircuits. Front Neural Circuits 2019; 13:34. [PMID: 31133821 PMCID: PMC6517540 DOI: 10.3389/fncir.2019.00034] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022] Open
Abstract
Histological studies of myelin-stained sectioned cadaver brain and in vivo myelin-weighted magnetic resonance imaging (MRI) show that the cerebral cortex is organized into cortical areas with generally well-defined boundaries, which have consistent internal patterns of myelination. The process of myelination is largely driven by neural experience, in which the axonal passage of action potentials stimulates neighboring oligodendrocytes to perform their task. This bootstrapping process, such that the traffic of action potentials facilitates increased traffic, suggests the hypothesis that the specific pattern of myelination (myeloarchitecture) in each cortical area reveals the principal cortical microcircuits required for the function of that area. If this idea is correct, the observable sequential maturation of specific brain areas can provide evidence for models of the stages of cognitive development.
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Affiliation(s)
- Robert Turner
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom
- Spinoza Centre for Neuroimaging, University of Amsterdam, Amsterdam, Netherlands
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27
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Lee HL, Li Z, Coulson EJ, Chuang KH. Ultrafast fMRI of the rodent brain using simultaneous multi-slice EPI. Neuroimage 2019; 195:48-58. [PMID: 30910726 DOI: 10.1016/j.neuroimage.2019.03.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/05/2019] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
Increasing spatial and temporal resolutions of functional MRI (fMRI) measurement has been shown to benefit the study of neural dynamics and functional interaction. However, acceleration of rodent brain fMRI using parallel and simultaneous multi-slice imaging techniques is hampered by the lack of high-density phased-array coils for the small brain. To overcome this limitation, we adapted phase-offset multiplanar and blipped-controlled aliasing echo planar imaging (EPI) to enable simultaneous multi-slice fMRI of the mouse brain using a single loop coil on a 9.4T scanner. Four slice bands of 0.3 × 0.3 × 0.5 mm3 resolution can be simultaneously acquired to cover the whole brain at a temporal resolution of 300 ms or the whole cerebrum in 150 ms. Instead of losing signal-to-noise ratio (SNR), both spatial and temporal SNR can be increased due to the increased k-space sampling compared to a standard single-band EPI. Task fMRI using a visual stimulation shows close to 80% increase of z-score and 4 times increase of activated area in the visual cortex using the multiband EPI due to the highly increased temporal samples. Resting-state fMRI shows reliable detection of bilateral connectivity by both single-band and multiband EPI, but no significant difference was found. Without the need of a dedicated hardware, we have demonstrated a practical method that can enable unparallelly fast whole-brain fMRI for preclinical studies. This technique can be used to increase sensitivity, distinguish transient response or acquire high spatiotemporal resolution fMRI.
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Affiliation(s)
- Hsu-Lei Lee
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia; Centre of Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Zengmin Li
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Elizabeth J Coulson
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Kai-Hsiang Chuang
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia; Centre of Advanced Imaging, The University of Queensland, Brisbane, Australia.
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28
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Chang M, Edmiston EK, Womer FY, Zhou Q, Wei S, Jiang X, Zhou Y, Ye Y, Huang H, Zuo XN, Xu K, Tang Y, Wang F. Spontaneous low-frequency fluctuations in the neural system for emotional perception in major psychiatric disorders: amplitude similarities and differences across frequency bands. J Psychiatry Neurosci 2019; 44:132-141. [PMID: 30810024 PMCID: PMC6397038 DOI: 10.1503/jpn.170226] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Growing evidence indicates both shared and distinct features of emotional perception in schizophrenia, bipolar disorder and major depressive disorder. In these disorders, alterations in spontaneous low-frequency fluctuations have been reported in the neural system for emotional perception, but the similarities and differences in the amplitude of low-frequency fluctuation (ALFF) across the 3 disorders are unknown. METHODS We compared ALFF and its signal balance in the neural system for emotional perception at 2 frequency bands (slow-5 and slow-4) in 119 participants with schizophrenia, 100 with bipolar disorder, 123 with major depressive disorder and 183 healthy controls. We performed exploratory Pearson partial correlation analyses to determine the relationship between ALFF signal balance and clinical variables. RESULTS We observed commonalities in ALFF change patterns across the 3 disorders for emotional perception neural substrates, such as increased ALFF in the anterior cerebrum (including subcortical, limbic, paralimbic and heteromodal cortical regions) and decreased ALFF in the posterior visual cortices. Schizophrenia, bipolar disorder and major depressive disorder showed significantly decreased ALFF signal balance in the neural system for emotional perception at both slow-5 and slow-4 frequency bands, with the greatest alterations for schizophrenia, followed by bipolar disorder and major depressive disorder. We found a negative correlation between ALFF signal balance and negative/disorganized symptoms in slow-4 across the 3 disorders. LIMITATIONS The relatively broad age range in our sample and the cross-sectional study design may not account for our findings. CONCLUSION The extent of the commonalities we observed further support the concept of core neurobiological disruptions shared among the 3 disorders; ALFF signal balance could be an important neuroimaging marker for the diagnosis and treatment of schizophrenia, bipolar disorder and major depressive disorder.
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Affiliation(s)
- Miao Chang
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Elliot K. Edmiston
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Fay Y. Womer
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Qian Zhou
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Shengnan Wei
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Xiaowei Jiang
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Yifang Zhou
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Yuting Ye
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Haiyan Huang
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Xi-Nian Zuo
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Ke Xu
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Yanqing Tang
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
| | - Fei Wang
- From the Department of Radiology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Jiang, Wang, Wei, Xu); the Department of Psychiatry, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Tang, Q. Zhou, Y. Zhou); the Brain Function Research Section, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, PR China (Chang, Edmiston, Jiang, Tang, Wang, Wei, Xu, Q. Zhou, Y. Zhou); the Department of Psychiatry, Washington University School of Medicine, St. Louis, MO (Womer); the Division of Biostatistics, University of California, Berkeley, Berkeley, CA (Huang, Ye); the CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, PR China (Zuo); and the Department of Psychology, University of Chinese Academy of Sciences, Beijing, PR China (Zuo)
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Gandhi R, Tsoumpas C. Preclinical Imaging Biomarkers for Postischaemic Neurovascular Remodelling. CONTRAST MEDIA & MOLECULAR IMAGING 2019; 2019:3128529. [PMID: 30863220 PMCID: PMC6378027 DOI: 10.1155/2019/3128529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/22/2018] [Accepted: 12/04/2018] [Indexed: 11/30/2022]
Abstract
In the pursuit of understanding the pathological alterations that underlie ischaemic injuries, such as vascular remodelling and reorganisation, there is a need for recognising the capabilities and limitations of in vivo imaging techniques. Thus, this review presents contemporary published research of imaging modalities that have been implemented to study postischaemic neurovascular changes in small animals. A comparison of the technical aspects of the various imaging tools is included to set the framework for identifying the most appropriate methods to observe postischaemic neurovascular remodelling. A systematic search of the PubMed® and Elsevier's Scopus databases identified studies that were conducted between 2008 and 2018 to explore postischaemic neurovascular remodelling in small animal models. Thirty-five relevant in vivo imaging studies are included, of which most made use of magnetic resonance imaging or positron emission tomography, whilst various optical modalities were also utilised. Notably, there is an increasing trend of using multimodal imaging to exploit the most beneficial properties of each imaging technique to elucidate different aspects of neurovascular remodelling. Nevertheless, there is still scope for further utilising noninvasive imaging tools such as contrast agents or radiotracers, which will have the ability to monitor neurovascular changes particularly during restorative therapy. This will facilitate more successful utility of the clinical imaging techniques in the interpretation of neurovascular reorganisation over time.
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Affiliation(s)
- Richa Gandhi
- Department of Biomedical Imaging Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9NL, West Yorkshire, UK
| | - Charalampos Tsoumpas
- Department of Biomedical Imaging Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9NL, West Yorkshire, UK
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30
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Mishra A, Majumdar S, Wang F, Wilson GH, Gore JC, Chen LM. Functional connectivity with cortical depth assessed by resting state fMRI of subregions of S1 in squirrel monkeys. Hum Brain Mapp 2019; 40:329-339. [PMID: 30251760 PMCID: PMC6289644 DOI: 10.1002/hbm.24375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/15/2022] Open
Abstract
Whereas resting state blood oxygenation-level dependent (BOLD) functional MRI has been widely used to assess functional connectivity between cortical regions, the laminar specificity of such measures is poorly understood. This study aims to determine: (a) whether the resting state functional connectivity (rsFC) between two functionally related cortical regions varies with cortical depth, (b) the relationship between layer-resolved tactile stimulus-evoked activation pattern and interlayer rsFC pattern between two functionally distinct but related somatosensory areas 3b and 1, and (c) the effects of spatial resolution on rsFC measures. We examined the interlayer rsFC between areas 3b and 1 of squirrel monkeys under anesthesia using tactile stimulus-driven and resting state BOLD acquisitions at submillimeter resolution. Consistent with previous observations in the areas 3b and 1, we detected robust stimulus-evoked BOLD activations with foci were confined mainly to the upper layers (centered at 21% of the cortical depth). By carefully placing seeds in upper, middle, and lower layers of areas 3b and 1, we observed strong rsFC between upper and middle layers of these two areas. The layer-resolved activation patterns in areas 3b and 1 agree with their interlayer rsFC patterns, and are consistent with the known anatomical connections between layers. In summary, using BOLD rsFC pattern, we identified an interlayer interareal microcircuit that shows strong intrinsic functional connections between upper and middle layer areas 3b and 1. RsFC can be used as a robust invasive tool to probe interlayer corticocortical microcircuits.
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Affiliation(s)
- Arabinda Mishra
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennessee
- Vanderbilt University Institute of Imaging ScienceVanderbilt UniversityNashvilleTennessee
| | - Shantanu Majumdar
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennessee
- Vanderbilt University Institute of Imaging ScienceVanderbilt UniversityNashvilleTennessee
| | - Feng Wang
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennessee
- Vanderbilt University Institute of Imaging ScienceVanderbilt UniversityNashvilleTennessee
| | - George H. Wilson
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennessee
- Vanderbilt University Institute of Imaging ScienceVanderbilt UniversityNashvilleTennessee
| | - John C. Gore
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennessee
- Vanderbilt University Institute of Imaging ScienceVanderbilt UniversityNashvilleTennessee
| | - Li Min Chen
- Department of Radiology and Radiological SciencesVanderbilt University Medical CenterNashvilleTennessee
- Vanderbilt University Institute of Imaging ScienceVanderbilt UniversityNashvilleTennessee
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31
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Kim SG. Biophysics of BOLD fMRI investigated with animal models. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 292:82-89. [PMID: 29705033 DOI: 10.1016/j.jmr.2018.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/14/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
The widely-used BOLD fMRI signal depends on various anatomical, physiological, and imaging parameters. Thus, it is important to examine its biophysical and physiological source in order to optimize, model and accurately interpret fMRI. Animal models have been used to investigate these issues to take systematic measurements and combine with conventional invasive approaches. Here, we reviewed and discussed multiple issues, including the echo time-dependent intravascular contribution and extravascular contributions, gradient-echo vs. spin-echo fMRI, the physiological source of BOLD fMRI, arterial vs. venous cerebral blood volume change, cerebral oxygen consumption change, and arterial oxygen saturation change. We then discuss future directions of animal fMRI and translation to human fMRI. Systematic biophysical BOLD fMRI studies provide insight into the modeling and interpretation of BOLD fMRI in animals and humans.
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Affiliation(s)
- Seong-Gi Kim
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
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32
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Marquardt I, Schneider M, Gulban OF, Ivanov D, Uludağ K. Cortical depth profiles of luminance contrast responses in human V1 and V2 using 7 T fMRI. Hum Brain Mapp 2018; 39:2812-2827. [PMID: 29575494 DOI: 10.1002/hbm.24042] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/23/2018] [Accepted: 03/05/2018] [Indexed: 12/31/2022] Open
Abstract
Neural activity in early visual cortex is modulated by luminance contrast. Cortical depth (i.e., laminar) contrast responses have been studied in monkey early visual cortex, but not in humans. In addition to the high spatial resolution needed and the ensuing low signal-to-noise ratio, laminar studies in humans using fMRI are hampered by the strong venous vascular weighting of the fMRI signal. In this study, we measured luminance contrast responses in human V1 and V2 with high-resolution fMRI at 7 T. To account for the effect of intracortical ascending veins, we applied a novel spatial deconvolution model to the fMRI depth profiles. Before spatial deconvolution, the contrast response in V1 showed a slight local maximum at mid cortical depth, whereas V2 exhibited a monotonic signal increase toward the cortical surface. After applying the deconvolution, both V1 and V2 showed a pronounced local maximum at mid cortical depth, with an additional peak in deep grey matter, especially in V1. Moreover, we found a difference in contrast sensitivity between V1 and V2, but no evidence for variations in contrast sensitivity as a function of cortical depth. These findings are in agreement with results obtained in nonhuman primates, but further research will be needed to validate the spatial deconvolution approach.
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Affiliation(s)
- Ingo Marquardt
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Marian Schneider
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Omer Faruk Gulban
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Dimo Ivanov
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Kâmil Uludağ
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
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33
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Kashyap S, Ivanov D, Havlicek M, Poser BA, Uludağ K. Impact of acquisition and analysis strategies on cortical depth-dependent fMRI. Neuroimage 2018; 168:332-344. [DOI: 10.1016/j.neuroimage.2017.05.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 03/31/2017] [Accepted: 05/11/2017] [Indexed: 01/19/2023] Open
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Linking brain vascular physiology to hemodynamic response in ultra-high field MRI. Neuroimage 2018; 168:279-295. [DOI: 10.1016/j.neuroimage.2017.02.063] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/05/2023] Open
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35
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Ultra-high field MRI: Advancing systems neuroscience towards mesoscopic human brain function. Neuroimage 2018; 168:345-357. [DOI: 10.1016/j.neuroimage.2017.01.028] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/06/2016] [Accepted: 01/12/2017] [Indexed: 01/26/2023] Open
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36
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Uğurbil K. Imaging at ultrahigh magnetic fields: History, challenges, and solutions. Neuroimage 2018; 168:7-32. [PMID: 28698108 PMCID: PMC5758441 DOI: 10.1016/j.neuroimage.2017.07.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 01/06/2023] Open
Abstract
Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and spectroscopy studies of humans at 4 T and animal models at 9.4 T, leading to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has provided numerous technological solutions to challenges posed at these ultrahigh fields, and demonstrated the existence of significant advantages in signal-to-noise ratio and biological information content. Primary difference from lower fields is the deviation from the near field regime at the radiofrequencies (RF) corresponding to hydrogen resonance conditions. At such ultrahigh fields, the RF is characterized by attenuated traveling waves in the human body, which leads to image non-uniformities for a given sample-coil configuration because of destructive and constructive interferences. These non-uniformities were initially considered detrimental to progress of imaging at high field strengths. However, they are advantageous for parallel imaging in signal reception and transmission, two critical technologies that account, to a large extend, for the success of ultrahigh fields. With these technologies and improvements in instrumentation and imaging methods, today ultrahigh fields have provided unprecedented gains in imaging of brain function and anatomy, and started to make inroads into investigation of the human torso and extremities. As extensive as they are, these gains still constitute a prelude to what is to come given the increasingly larger effort committed to ultrahigh field research and development of ever better instrumentation and techniques.
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Affiliation(s)
- Kamil Uğurbil
- Center for Magnetic Resonance Research (CMRR), University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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37
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Vu AT, Beckett A, Setsompop K, Feinberg DA. Evaluation of SLIce Dithered Enhanced Resolution Simultaneous MultiSlice (SLIDER-SMS) for human fMRI. Neuroimage 2018; 164:164-171. [PMID: 28185951 PMCID: PMC5547021 DOI: 10.1016/j.neuroimage.2017.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/19/2017] [Accepted: 02/01/2017] [Indexed: 11/22/2022] Open
Abstract
High isotropic resolution fMRI is challenging primarily due to long repetition times (TR) and insufficient SNR, especially at lower field strengths. Recently, Simultaneous Multi-Slice (SMS) imaging with blipped-CAIPI has substantially reduced scan time and improved SNR efficiency of fMRI. Similarly, super-resolution techniques utilizing sub- voxel spatial shifts in the slice direction have increased both resolution and SNR efficiency. Here we demonstrate the synergistic combination of SLIce Dithered Enhanced Resolution (SLIDER) and SMS for high-resolution, high-SNR whole brain fMRI in comparison to standard resolution fMRI data as well as high-resolution data. With SLIDER-SMS, high spatial frequency information is recovered (unaliased) even in absence of super-resolution deblurring algorithms. Additionally we find that BOLD CNR (as measured by t-value in a visual checkerboard paradigm) is improved by as much as 100% relative to traditionally acquired high- resolution data. Using this gain in CNR, we are able to obtain unprecedented nominally isotropic resolutions at 3T (0.66 mm) and 7T (0.45 mm).
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Affiliation(s)
- An T Vu
- San Francisco VA Health Care System, Center for Imaging of Neurodegenerative Disease, San Francisco, CA, United States; University of California, Berkeley, Berkeley, CA, United States; Advanced MRI Technologies, Sebastopol, CA, United States.
| | - Alex Beckett
- University of California, Berkeley, Berkeley, CA, United States; Advanced MRI Technologies, Sebastopol, CA, United States
| | - Kawin Setsompop
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital Charlestown, MA, United States
| | - David A Feinberg
- University of California, Berkeley, Berkeley, CA, United States; Advanced MRI Technologies, Sebastopol, CA, United States
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38
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Huber L, Ivanov D, Handwerker DA, Marrett S, Guidi M, Uludağ K, Bandettini PA, Poser BA. Techniques for blood volume fMRI with VASO: From low-resolution mapping towards sub-millimeter layer-dependent applications. Neuroimage 2018; 164:131-143. [PMID: 27867088 PMCID: PMC5436958 DOI: 10.1016/j.neuroimage.2016.11.039] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/24/2016] [Accepted: 11/14/2016] [Indexed: 12/24/2022] Open
Abstract
Quantitative cerebral blood volume (CBV) fMRI has the potential to overcome several specific limitations of BOLD fMRI. It provides direct physiological interpretability and promises superior localization specificity in applications of sub-millimeter resolution fMRI applications at ultra-high magnetic fields (7T and higher). Non-invasive CBV fMRI using VASO (vascular space occupancy), however, is inherently limited with respect to its data acquisition efficiency, restricting its imaging coverage and achievable spatial and temporal resolution. This limitation may be reduced with recent advanced acceleration and reconstruction strategies that allow two-dimensional acceleration, such as in simultaneous multi-slice (SMS) 2D-EPI or 3D-EPI in combination with CAIPIRINHA field-of-view shifting. In this study, we sought to determine the functional sensitivity and specificity of these readout strategies with VASO over a broad range of spatial resolutions; spanning from low spatial resolution (3mm) whole-cortex to sub-millimeter (0.75mm) slab-of-cortex (for cortical layer-dependent applications). In the thermal-noise-dominated regime of sub-millimeter resolutions, 3D-EPI-VASO provides higher temporal stability and sensitivity to detect changes in CBV compared to 2D-EPI-VASO. In this regime, 3D-EPI-VASO unveils task activation located in the cortical laminae with little contamination from surface veins, in contrast to the cortical surface weighting of GE-BOLD fMRI. In the physiological-noise-dominated regime of lower resolutions, however, 2D-SMS-VASO shows superior performance compared to 3D-EPI-VASO. Due to its superior sensitivity at a layer-dependent level, 3D-EPI VASO promises to play an important role in future neuroscientific applications of layer-dependent fMRI.
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Affiliation(s)
- Laurentius Huber
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, NIMH, NIH, Bethesda, MD, USA.
| | - Dimo Ivanov
- Maastricht Brain Imaging Centre, Faculty of Psychology and Neurosciencve, Maastricht University, Maastricht, The Netherlands
| | - Daniel A Handwerker
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, NIMH, NIH, Bethesda, MD, USA
| | | | - Maria Guidi
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Kâmil Uludağ
- Maastricht Brain Imaging Centre, Faculty of Psychology and Neurosciencve, Maastricht University, Maastricht, The Netherlands
| | - Peter A Bandettini
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, NIMH, NIH, Bethesda, MD, USA; FMRIF, NIMH, NIH, Bethesda, MD, USA
| | - Benedikt A Poser
- Maastricht Brain Imaging Centre, Faculty of Psychology and Neurosciencve, Maastricht University, Maastricht, The Netherlands
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39
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Li X, Zhu Q, Janssens T, Arsenault JT, Vanduffel W. In Vivo Identification of Thick, Thin, and Pale Stripes of Macaque Area V2 Using Submillimeter Resolution (f)MRI at 3 T. Cereb Cortex 2017; 29:544-560. [DOI: 10.1093/cercor/bhx337] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/29/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xiaolian Li
- Laboratory of Neuro- and Psychophysiology, Department of Neurosciences, KU Leuven Medical School, Leuven, Belgium
| | - Qi Zhu
- Laboratory of Neuro- and Psychophysiology, Department of Neurosciences, KU Leuven Medical School, Leuven, Belgium
| | - Thomas Janssens
- Laboratory of Neuro- and Psychophysiology, Department of Neurosciences, KU Leuven Medical School, Leuven, Belgium
- Current address: Siemens Healthcare Belgium, Beersel, Belgium
| | - John T Arsenault
- Laboratory of Neuro- and Psychophysiology, Department of Neurosciences, KU Leuven Medical School, Leuven, Belgium
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Wim Vanduffel
- Laboratory of Neuro- and Psychophysiology, Department of Neurosciences, KU Leuven Medical School, Leuven, Belgium
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
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40
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Huber L, Handwerker DA, Jangraw DC, Chen G, Hall A, Stüber C, Gonzalez-Castillo J, Ivanov D, Marrett S, Guidi M, Goense J, Poser BA, Bandettini PA. High-Resolution CBV-fMRI Allows Mapping of Laminar Activity and Connectivity of Cortical Input and Output in Human M1. Neuron 2017; 96:1253-1263.e7. [PMID: 29224727 DOI: 10.1016/j.neuron.2017.11.005] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/25/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
Abstract
Layer-dependent fMRI allows measurements of information flow in cortical circuits, as afferent and efferent connections terminate in different cortical layers. However, it is unknown to what level human fMRI is specific and sensitive enough to reveal directional functional activity across layers. To answer this question, we developed acquisition and analysis methods for blood-oxygen-level-dependent (BOLD) and cerebral-blood-volume (CBV)-based laminar fMRI and used these to discriminate four different tasks in the human motor cortex (M1). In agreement with anatomical data from animal studies, we found evidence for somatosensory and premotor input in superficial layers of M1 and for cortico-spinal motor output in deep layers. Laminar resting-state fMRI showed directional functional connectivity of M1 with somatosensory and premotor areas. Our findings demonstrate that CBV-fMRI can be used to investigate cortical activity in humans with unprecedented detail, allowing investigations of information flow between brain regions and outperforming conventional BOLD results that are often buried under vascular biases.
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Affiliation(s)
| | | | | | | | | | - Carsten Stüber
- Department of Radiology, Weill Cornell Medical College, New York, NY 10044, USA; Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT 06511, USA
| | | | - Dimo Ivanov
- Maastricht Brain Imaging Centre, Maastricht University, Maastricht 6229, the Netherlands
| | | | - Maria Guidi
- NMR Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany
| | - Jozien Goense
- School of Psychology and Institute of Neuroscience and Psychology, University of Glasgow, Glasgow G12 8QB, UK
| | - Benedikt A Poser
- Maastricht Brain Imaging Centre, Maastricht University, Maastricht 6229, the Netherlands
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41
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Petridou N, Siero JCW. Laminar fMRI: What can the time domain tell us? Neuroimage 2017; 197:761-771. [PMID: 28736308 DOI: 10.1016/j.neuroimage.2017.07.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/06/2017] [Accepted: 07/19/2017] [Indexed: 01/30/2023] Open
Abstract
The rapid developments in functional MRI (fMRI) acquisition methods and hardware technologies in recent years, particularly at high field (≥7 T), have enabled unparalleled visualization of functional detail at a laminar or columnar level, bringing fMRI close to the intrinsic resolution of brain function. These advances highlight the potential of high resolution fMRI to be a valuable tool to study the fundamental processing performed in cortical micro-circuits, and their interactions such as feedforward and feedback processes. Notably, because fMRI measures neuronal activity via hemodynamics, the ultimate resolution it affords depends on the spatial specificity of hemodynamics to neuronal activity at a detailed spatial scale, and by the evolution of this specificity over time. Several laminar (≤1 mm spatial resolution) fMRI studies have examined spatial characteristics of the measured hemodynamic signals across cortical depth, in light of understanding or improving the spatial specificity of laminar fMRI. Few studies have examined temporal features of the hemodynamic response across cortical depth. Temporal features of the hemodynamic response offer an additional means to improve the specificity of fMRI, and could help target neuronal processes and neurovascular coupling relationships across laminae, for example by differences in the onset times of the response across cortical depth. In this review, we discuss factors that affect the timing of neuronal and hemodynamic responses across laminae, touching on the neuronal laminar organization, and focusing on the laminar vascular organization. We provide an overview of hemodynamics across the cortical vascular tree based on optical imaging studies, and review temporal aspects of hemodynamics that have been examined across cortical depth in high spatiotemporal resolution fMRI studies. Last, we discuss the limits and potential of high spatiotemporal resolution fMRI to study laminar neurovascular coupling and neuronal processes.
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Affiliation(s)
- Natalia Petridou
- Radiology, University Medical Centre Utrecht, Utrecht, The Netherlands.
| | - Jeroen C W Siero
- Radiology, University Medical Centre Utrecht, Utrecht, The Netherlands; Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands
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42
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Poplawsky AJ, Fukuda M, Kim SG. Foundations of layer-specific fMRI and investigations of neurophysiological activity in the laminarized neocortex and olfactory bulb of animal models. Neuroimage 2017; 199:718-729. [PMID: 28502845 DOI: 10.1016/j.neuroimage.2017.05.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/02/2017] [Accepted: 05/11/2017] [Indexed: 12/25/2022] Open
Abstract
Laminar organization of neuronal circuits is a recurring feature of how the brain processes information. For instance, different layers compartmentalize different cell types, synaptic activities, and have unique intrinsic and extrinsic connections that serve as units for specialized signal processing. Functional MRI is an invaluable tool to investigate laminar processing in the in vivo human brain, but it measures neuronal activity indirectly by way of the hemodynamic response. Therefore, the accuracy of high-resolution laminar fMRI depends on how precisely it can measure localized microvascular changes nearest to the site of evoked activity. To determine the specificity of fMRI responses to the true neurophysiological responses across layers, the flexibility to invasive procedures in animal models has been necessary. In this review, we will examine different fMRI contrasts and their appropriate uses for layer-specific fMRI, and how localized laminar processing was examined in the neocortex and olfactory bulb. Through collective efforts, it was determined that microvessels, including capillaries, are regulated within single layers and that several endogenous and contrast-enhanced fMRI contrast mechanisms can separate these neural-specific vascular changes from the nonspecific, especially cerebral blood volume-weighted fMRI with intravenous contrast agent injection. We will also propose some open questions that are relevant for the successful implementation of layer-specific fMRI and its potential future directions to study laminar processing when combined with optogenetics.
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Affiliation(s)
- Alexander John Poplawsky
- Neuroimaging Laboratory, Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Mitsuhiro Fukuda
- Neuroimaging Laboratory, Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seong-Gi Kim
- Center for Neuroscience Imaging Research, Institute of Basic Science, Suwon 440-746, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea
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43
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Cortical Representation of Pain and Touch: Evidence from Combined Functional Neuroimaging and Electrophysiology in Non-human Primates. Neurosci Bull 2017; 34:165-177. [PMID: 28466257 DOI: 10.1007/s12264-017-0133-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
Human functional MRI studies in acute and various chronic pain conditions have revolutionized how we view pain, and have led to a new theory that complex multi-dimensional pain experience (sensory-discriminative, affective/motivational, and cognitive) is represented by concurrent activity in widely-distributed brain regions (termed a network or pain matrix). Despite these breakthrough discoveries, the specific functions proposed for these regions remain elusive, because detailed electrophysiological characterizations of these regions in the primate brain are lacking. To fill in this knowledge gap, we have studied the cortical areas around the central and lateral sulci of the non-human primate brain with combined submillimeter resolution functional imaging (optical imaging and fMRI) and intracranial electrophysiological recording. In this mini-review, I summarize and present data showing that the cortical circuitry engaged in nociceptive processing is much more complex than previously recognized. Electrophysiological evidence supports the engagement of a distinct nociceptive-processing network within SI (i.e., areas 3a, 3b, 1 and 2), SII, and other areas along the lateral sulcus. Deafferentation caused by spinal cord injury profoundly alters the relationships between fMRI and electrophysiological signals. This finding has significant implications for using fMRI to study chronic pain conditions involving deafferentation in humans.
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44
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Moerel M, De Martino F, Kemper VG, Schmitter S, Vu AT, Uğurbil K, Formisano E, Yacoub E. Sensitivity and specificity considerations for fMRI encoding, decoding, and mapping of auditory cortex at ultra-high field. Neuroimage 2017; 164:18-31. [PMID: 28373123 DOI: 10.1016/j.neuroimage.2017.03.063] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 12/18/2016] [Accepted: 03/29/2017] [Indexed: 01/05/2023] Open
Abstract
Following rapid technological advances, ultra-high field functional MRI (fMRI) enables exploring correlates of neuronal population activity at an increasing spatial resolution. However, as the fMRI blood-oxygenation-level-dependent (BOLD) contrast is a vascular signal, the spatial specificity of fMRI data is ultimately determined by the characteristics of the underlying vasculature. At 7T, fMRI measurement parameters determine the relative contribution of the macro- and microvasculature to the acquired signal. Here we investigate how these parameters affect relevant high-end fMRI analyses such as encoding, decoding, and submillimeter mapping of voxel preferences in the human auditory cortex. Specifically, we compare a T2* weighted fMRI dataset, obtained with 2D gradient echo (GE) EPI, to a predominantly T2 weighted dataset obtained with 3D GRASE. We first investigated the decoding accuracy based on two encoding models that represented different hypotheses about auditory cortical processing. This encoding/decoding analysis profited from the large spatial coverage and sensitivity of the T2* weighted acquisitions, as evidenced by a significantly higher prediction accuracy in the GE-EPI dataset compared to the 3D GRASE dataset for both encoding models. The main disadvantage of the T2* weighted GE-EPI dataset for encoding/decoding analyses was that the prediction accuracy exhibited cortical depth dependent vascular biases. However, we propose that the comparison of prediction accuracy across the different encoding models may be used as a post processing technique to salvage the spatial interpretability of the GE-EPI cortical depth-dependent prediction accuracy. Second, we explored the mapping of voxel preferences. Large-scale maps of frequency preference (i.e., tonotopy) were similar across datasets, yet the GE-EPI dataset was preferable due to its larger spatial coverage and sensitivity. However, submillimeter tonotopy maps revealed biases in assigned frequency preference and selectivity for the GE-EPI dataset, but not for the 3D GRASE dataset. Thus, a T2 weighted acquisition is recommended if high specificity in tonotopic maps is required. In conclusion, different fMRI acquisitions were better suited for different analyses. It is therefore critical that any sequence parameter optimization considers the eventual intended fMRI analyses and the nature of the neuroscience questions being asked.
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Affiliation(s)
- Michelle Moerel
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Federico De Martino
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Valentin G Kemper
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Sebastian Schmitter
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Department of Biomedical Magnetic Resonance, Physikalisch-Technische Bundesanstalt, Berlin, Germany.
| | - An T Vu
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA; Advanced MRI Technologies, Sebastopol, CA, USA.
| | - Kâmil Uğurbil
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA.
| | - Elia Formisano
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands; Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands; Maastricht Brain Imaging Center (MBIC), Maastricht, The Netherlands.
| | - Essa Yacoub
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA.
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45
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Strappini F, Gilboa E, Pitzalis S, Kay K, McAvoy M, Nehorai A, Snyder AZ. Adaptive smoothing based on Gaussian processes regression increases the sensitivity and specificity of fMRI data. Hum Brain Mapp 2016; 38:1438-1459. [PMID: 27943516 DOI: 10.1002/hbm.23464] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 10/21/2016] [Accepted: 11/01/2016] [Indexed: 11/11/2022] Open
Abstract
Temporal and spatial filtering of fMRI data is often used to improve statistical power. However, conventional methods, such as smoothing with fixed-width Gaussian filters, remove fine-scale structure in the data, necessitating a tradeoff between sensitivity and specificity. Specifically, smoothing may increase sensitivity (reduce noise and increase statistical power) but at the cost loss of specificity in that fine-scale structure in neural activity patterns is lost. Here, we propose an alternative smoothing method based on Gaussian processes (GP) regression for single subjects fMRI experiments. This method adapts the level of smoothing on a voxel by voxel basis according to the characteristics of the local neural activity patterns. GP-based fMRI analysis has been heretofore impractical owing to computational demands. Here, we demonstrate a new implementation of GP that makes it possible to handle the massive data dimensionality of the typical fMRI experiment. We demonstrate how GP can be used as a drop-in replacement to conventional preprocessing steps for temporal and spatial smoothing in a standard fMRI pipeline. We present simulated and experimental results that show the increased sensitivity and specificity compared to conventional smoothing strategies. Hum Brain Mapp 38:1438-1459, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Francesca Strappini
- Department of Neurology, Washington University in Saint Louis, School of Medicine, Saint Louis, Missouri.,Neurobiology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elad Gilboa
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri.,Department of Electrical Engineering, Technion Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sabrina Pitzalis
- Cognitive and Motor Rehabilitation Unit, Santa Lucia Foundation, Rome, 00179, Italy.,Department of Motor, Human and Health Sciences, University of Rome "Foro Italico,", Rome, 00194, Italy
| | - Kendrick Kay
- Department of Psychology, Washington University in Saint Louis, School of Medicine, Saint Louis, Missouri.,Department of Radiology, University of Minnesota Twin Cities, Minneapolis, Minnesota
| | - Mark McAvoy
- Department of Radiology, Washington University in Saint Louis, School of Medicine, Saint Louis, Missouri
| | - Arye Nehorai
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri
| | - Abraham Z Snyder
- Department of Neurology, Washington University in Saint Louis, School of Medicine, Saint Louis, Missouri.,Department of Radiology, Washington University in Saint Louis, School of Medicine, Saint Louis, Missouri
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46
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T Vu A, Jamison K, Glasser MF, Smith SM, Coalson T, Moeller S, Auerbach EJ, Uğurbil K, Yacoub E. Tradeoffs in pushing the spatial resolution of fMRI for the 7T Human Connectome Project. Neuroimage 2016; 154:23-32. [PMID: 27894889 DOI: 10.1016/j.neuroimage.2016.11.049] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/07/2016] [Accepted: 11/19/2016] [Indexed: 11/28/2022] Open
Abstract
Whole-brain functional magnetic resonance imaging (fMRI), in conjunction with multiband acceleration, has played an important role in mapping the functional connectivity throughout the entire brain with both high temporal and spatial resolution. Ultrahigh magnetic field strengths (7T and above) allow functional imaging with even higher functional contrast-to-noise ratios for improved spatial resolution and specificity compared to traditional field strengths (1.5T and 3T). High-resolution 7T fMRI, however, has primarily been constrained to smaller brain regions given the amount of time it takes to acquire the number of slices necessary for high resolution whole brain imaging. Here we evaluate a range of whole-brain high-resolution resting state fMRI protocols (0.9, 1.25, 1.5, 1.6 and 2mm isotropic voxels) at 7T, obtained with both in-plane and slice acceleration parallel imaging techniques to maintain the temporal resolution and brain coverage typically acquired at 3T. Using the processing pipeline developed by the Human Connectome Project, we demonstrate that high resolution images acquired at 7T provide increased functional contrast to noise ratios with significantly less partial volume effects and more distinct spatial features, potentially allowing for robust individual subject parcellations and descriptions of fine-scaled patterns, such as visuotopic organization.
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Affiliation(s)
- An T Vu
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA; Helen Wills Institute for Neuroscience, University of California, Berkeley, CA, USA; Advanced MRI Technologies, Sebastopol, CA, USA.
| | - Keith Jamison
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Matthew F Glasser
- Washington University School of Medicine, Washington University, St. Louis, MO, USA
| | - Stephen M Smith
- FMRIB (Oxford Centre for Functional MRI of the Brain), Oxford University, Oxford, UK
| | - Timothy Coalson
- Washington University School of Medicine, Washington University, St. Louis, MO, USA
| | - Steen Moeller
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Edward J Auerbach
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Kamil Uğurbil
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA
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Intracortical depth analyses of frequency-sensitive regions of human auditory cortex using 7TfMRI. Neuroimage 2016; 143:116-127. [PMID: 27608603 DOI: 10.1016/j.neuroimage.2016.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/15/2016] [Accepted: 09/04/2016] [Indexed: 11/23/2022] Open
Abstract
Despite recent advances in auditory neuroscience, the exact functional organization of human auditory cortex (AC) has been difficult to investigate. Here, using reversals of tonotopic gradients as the test case, we examined whether human ACs can be more precisely mapped by avoiding signals caused by large draining vessels near the pial surface, which bias blood-oxygen level dependent (BOLD) signals away from the actual sites of neuronal activity. Using ultra-high field (7T) fMRI and cortical depth analysis techniques previously applied in visual cortices, we sampled 1mm isotropic voxels from different depths of AC during narrow-band sound stimulation with biologically relevant temporal patterns. At the group level, analyses that considered voxels from all cortical depths, but excluded those intersecting the pial surface, showed (a) the greatest statistical sensitivity in contrasts between activations to high vs. low frequency sounds and (b) the highest inter-subject consistency of phase-encoded continuous tonotopy mapping. Analyses based solely on voxels intersecting the pial surface produced the least consistent group results, even when compared to analyses based solely on voxels intersecting the white-matter surface where both signal strength and within-subject statistical power are weakest. However, no evidence was found for reduced within-subject reliability in analyses considering the pial voxels only. Our group results could, thus, reflect improved inter-subject correspondence of high and low frequency gradients after the signals from voxels near the pial surface are excluded. Using tonotopy analyses as the test case, our results demonstrate that when the major physiological and anatomical biases imparted by the vasculature are controlled, functional mapping of human ACs becomes more consistent from subject to subject than previously thought.
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Systematic variation of population receptive field properties across cortical depth in human visual cortex. Neuroimage 2016; 139:427-438. [PMID: 27374728 DOI: 10.1016/j.neuroimage.2016.06.048] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 06/06/2016] [Accepted: 06/24/2016] [Indexed: 01/17/2023] Open
Abstract
Receptive fields (RFs) in visual cortex are organized in antagonistic, center-surround, configurations. RF properties change systematically across eccentricity and between visual field maps. However, it is unknown how center-surround configurations are organized in human visual cortex across lamina. We use sub-millimeter resolution functional MRI at 7Tesla and population receptive field (pRF) modeling to investigate the pRF properties in primary visual cortex (V1) across cortical depth. pRF size varies according to a U-shaped function, indicating smaller pRF center size in the middle compared to superficial and deeper intra-cortical portions of V1, consistent with non-human primate neurophysiological measurements. Moreover, a similar U-shaped function is also observed for pRF surround size. However, pRF center-surround ratio remains constant across cortical depth. Simulations suggest that this pattern of results can be directly linked to the flow of signals across cortical depth, with the visual input reaching the middle of cortical depth and then spreading towards superficial and deeper layers of V1. Conversely, blood-oxygenation-level-dependent (BOLD) signal amplitude increases monotonically towards the pial surface, in line with the known vascular organization across cortical depth. Independent estimates of the haemodynamic response function (HRF) across cortical depth show that the center-surround pRF size estimates across cortical depth cannot be explained by variations in the full-width half maximum (FWHM) of the HRF.
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Goense J, Bohraus Y, Logothetis NK. fMRI at High Spatial Resolution: Implications for BOLD-Models. Front Comput Neurosci 2016; 10:66. [PMID: 27445782 PMCID: PMC4923185 DOI: 10.3389/fncom.2016.00066] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/15/2016] [Indexed: 11/13/2022] Open
Abstract
As high-resolution functional magnetic resonance imaging (fMRI) and fMRI of cortical layers become more widely used, the question how well high-resolution fMRI signals reflect the underlying neural processing, and how to interpret laminar fMRI data becomes more and more relevant. High-resolution fMRI has shown laminar differences in cerebral blood flow (CBF), volume (CBV), and neurovascular coupling. Features and processes that were previously lumped into a single voxel become spatially distinct at high resolution. These features can be vascular compartments such as veins, arteries, and capillaries, or cortical layers and columns, which can have differences in metabolism. Mesoscopic models of the blood oxygenation level dependent (BOLD) response therefore need to be expanded, for instance, to incorporate laminar differences in the coupling between neural activity, metabolism and the hemodynamic response. Here we discuss biological and methodological factors that affect the modeling and interpretation of high-resolution fMRI data. We also illustrate with examples from neuropharmacology and the negative BOLD response how combining BOLD with CBF- and CBV-based fMRI methods can provide additional information about neurovascular coupling, and can aid modeling and interpretation of high-resolution fMRI.
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Affiliation(s)
- Jozien Goense
- Department of Psychology, Institute of Neuroscience and Psychology, University of Glasgow Glasgow, UK
| | - Yvette Bohraus
- Department of Physiology of Cognitive Processes, Max-Planck Institute for Biological Cybernetics Tübingen, Germany
| | - Nikos K Logothetis
- Department of Physiology of Cognitive Processes, Max-Planck Institute for Biological CyberneticsTübingen, Germany; Divison of Imaging Science and Biomedical Engineering, University of ManchesterManchester, UK
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