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Yun SD, Küppers F, Shah NJ. Submillimeter fMRI Acquisition Techniques for Detection of Laminar and Columnar Level Brain Activation. J Magn Reson Imaging 2024; 59:747-766. [PMID: 37589385 DOI: 10.1002/jmri.28911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Since the first demonstration in the early 1990s, functional MRI (fMRI) has emerged as one of the most powerful, noninvasive neuroimaging tools to probe brain functions. Subsequently, fMRI techniques have advanced remarkably, enabling the acquisition of functional signals with a submillimeter voxel size. This innovation has opened the possibility of investigating subcortical neural activities with respect to the cortical depths or cortical columns. For this purpose, numerous previous works have endeavored to design suitable functional contrast mechanisms and dedicated imaging techniques. Depending on the choice of the functional contrast, functional signals can be detected with high sensitivity or with improved spatial specificity to the actual activation site, and the pertaining issues have been discussed in a number of earlier works. This review paper primarily aims to provide an overview of the subcortical fMRI techniques that allow the acquisition of functional signals with a submillimeter resolution. Here, the advantages and disadvantages of the imaging techniques will be described and compared. We also summarize supplementary imaging techniques that assist in the analysis of the subcortical brain activation for more accurate mapping with reduced geometric deformation. This review suggests that there is no single universally accepted method as the gold standard for subcortical fMRI. Instead, the functional contrast and the corresponding readout imaging technique should be carefully determined depending on the purpose of the study. Due to the technical limitations of current fMRI techniques, most subcortical fMRI studies have only targeted partial brain regions. As a future prospect, the spatiotemporal resolution of fMRI will be pushed to satisfy the community's need for a deeper understanding of whole-brain functions and the underlying connectivity in order to achieve the ultimate goal of a time-resolved and layer-specific spatial scale. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 1.
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Affiliation(s)
- Seong Dae Yun
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
| | - Fabian Küppers
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
- RWTH Aachen University, Aachen, Germany
- Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany
- JARA - BRAIN - Translational Medicine, Aachen, Germany
- Department of Neurology, RWTH Aachen University, Aachen, Germany
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Kim H, Park S, Hu R, Hoang KB, Sun PZ. 3D CEST MRI with an unevenly segmented RF irradiation scheme: A feasibility study in brain tumor imaging. Magn Reson Med 2023; 90:2400-2410. [PMID: 37526017 PMCID: PMC10586718 DOI: 10.1002/mrm.29810] [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: 12/02/2022] [Revised: 06/17/2023] [Accepted: 07/08/2023] [Indexed: 08/02/2023]
Abstract
PURPOSE To integrate 3D CEST EPI with an unevenly segmented RF irradiation module and preliminarily demonstrate it in the clinical setting. METHODS A CEST MRI with unevenly segmented RF saturation was implemented, including a long primary RF saturation to induce the steady-state CEST effect, maintained with repetitive short secondary RF irradiation between readouts. This configuration reduces relaxation-induced blur artifacts during acquisition, allowing fast 3D spatial coverage. Numerical simulations were performed to select parameters such as flip angle (FA), short RF saturation duration (Ts2), and the number of readout segments. The sequence was validated experimentally with data from a phantom, healthy volunteers, and a brain tumor patient. RESULTS Based on the numerical simulation and l-carnosine gel phantom experiment, FA, Ts2, and the number of segments were set to 20°, 0.3 s, and the range from 4 to 8, respectively. The proposed method minimized signal modulation in the human brain images in the kz direction during the acquisition and provided the blur artifacts-free CEST contrast over the whole volume. Additionally, the CEST contrast in the tumor tissue region is higher than in the contralateral normal tissue region. CONCLUSIONS It is feasible to implement a highly accelerated 3D EPI CEST imaging with unevenly segmented RF irradiation.
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Affiliation(s)
- Hahnsung Kim
- Emory National Primate Research Center, Emory University, Atlanta GA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta GA
| | - Suhyung Park
- Department of Computer Engineering, Chonnam National University, South Korea
- Department of ICT Convergence System Engineering, Chonnam National University, South Korea
| | - Ranliang Hu
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta GA
| | - Kimberly B Hoang
- Department of Neurosurgery, Emory University School of Medicine, Atlanta GA
| | - Phillip Zhe Sun
- Emory National Primate Research Center, Emory University, Atlanta GA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta GA
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Feinberg DA, Beckett AJS, Vu AT, Stockmann J, Huber L, Ma S, Ahn S, Setsompop K, Cao X, Park S, Liu C, Wald LL, Polimeni JR, Mareyam A, Gruber B, Stirnberg R, Liao C, Yacoub E, Davids M, Bell P, Rummert E, Koehler M, Potthast A, Gonzalez-Insua I, Stocker S, Gunamony S, Dietz P. Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla. Nat Methods 2023; 20:2048-2057. [PMID: 38012321 PMCID: PMC10703687 DOI: 10.1038/s41592-023-02068-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 10/09/2023] [Indexed: 11/29/2023]
Abstract
To increase granularity in human neuroimaging science, we designed and built a next-generation 7 Tesla magnetic resonance imaging scanner to reach ultra-high resolution by implementing several advances in hardware. To improve spatial encoding and increase the image signal-to-noise ratio, we developed a head-only asymmetric gradient coil (200 mT m-1, 900 T m-1s-1) with an additional third layer of windings. We integrated a 128-channel receiver system with 64- and 96-channel receiver coil arrays to boost signal in the cerebral cortex while reducing g-factor noise to enable higher accelerations. A 16-channel transmit system reduced power deposition and improved image uniformity. The scanner routinely performs functional imaging studies at 0.35-0.45 mm isotropic spatial resolution to reveal cortical layer functional activity, achieves high angular resolution in diffusion imaging and reduces acquisition time for both functional and structural imaging.
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Affiliation(s)
- David A Feinberg
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
- Advanced MRI Technologies, Sebastopol, CA, USA.
| | - Alexander J S Beckett
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Advanced MRI Technologies, Sebastopol, CA, USA
| | - An T Vu
- Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veteran Affairs Health Care System, San Francisco, CA, USA
| | - Jason Stockmann
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Laurentius Huber
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | | | | | - Kawin Setsompop
- Radiological Sciences Laboratory, Stanford University, Stanford, CA, USA
| | - Xiaozhi Cao
- Radiological Sciences Laboratory, Stanford University, Stanford, CA, USA
| | - Suhyung Park
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Computer Engineering, Chonnam National University, Gwangju, Republic of Korea
- Department of ICT Convergence System Engineering, Chonnam National University, Gwangju, Republic of Korea
| | - Chunlei Liu
- Erwin Hahn 7T MRI Laboratory, Henry H. Wheeler Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Lawrence L Wald
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Jonathan R Polimeni
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Azma Mareyam
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Bernhard Gruber
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
- BARNLabs, Muenzkirchen, Austria
| | | | - Congyu Liao
- Radiological Sciences Laboratory, Stanford University, Stanford, CA, USA
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Mathias Davids
- A. A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
- Computer Assisted Clinical Medicine, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Paul Bell
- Siemens Medical Solutions, Malvern, PA, USA
| | | | | | | | | | | | - Shajan Gunamony
- Imaging Centre of Excellence, University of Glasgow, Glasgow, UK
- MR CoilTech Limited, Glasgow, UK
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Watakabe A, Skibbe H, Nakae K, Abe H, Ichinohe N, Rachmadi MF, Wang J, Takaji M, Mizukami H, Woodward A, Gong R, Hata J, Van Essen DC, Okano H, Ishii S, Yamamori T. Local and long-distance organization of prefrontal cortex circuits in the marmoset brain. Neuron 2023; 111:2258-2273.e10. [PMID: 37196659 PMCID: PMC10789578 DOI: 10.1016/j.neuron.2023.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/13/2023] [Accepted: 04/25/2023] [Indexed: 05/19/2023]
Abstract
The prefrontal cortex (PFC) has dramatically expanded in primates, but its organization and interactions with other brain regions are only partially understood. We performed high-resolution connectomic mapping of the marmoset PFC and found two contrasting corticocortical and corticostriatal projection patterns: "patchy" projections that formed many columns of submillimeter scale in nearby and distant regions and "diffuse" projections that spread widely across the cortex and striatum. Parcellation-free analyses revealed representations of PFC gradients in these projections' local and global distribution patterns. We also demonstrated column-scale precision of reciprocal corticocortical connectivity, suggesting that PFC contains a mosaic of discrete columns. Diffuse projections showed considerable diversity in the laminar patterns of axonal spread. Altogether, these fine-grained analyses reveal important principles of local and long-distance PFC circuits in marmosets and provide insights into the functional organization of the primate brain.
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Affiliation(s)
- Akiya Watakabe
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Laboratory for Haptic Perception and Cognitive Physiology, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Henrik Skibbe
- Brain Image Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Ken Nakae
- Integrated Systems Biology Laboratory, Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Kyoto 606-8501, Japan; Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Hiroshi Abe
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Laboratory for Haptic Perception and Cognitive Physiology, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Noritaka Ichinohe
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-0031, Japan
| | - Muhammad Febrian Rachmadi
- Brain Image Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Faculty of Computer Science, Universitas Indonesia, Depok, Jawa Barat 16424, Indonesia
| | - Jian Wang
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Masafumi Takaji
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Laboratory for Haptic Perception and Cognitive Physiology, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Alexander Woodward
- Connectome Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Rui Gong
- Connectome Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Junichi Hata
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo 116-8551, Japan
| | - David C Van Essen
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hideyuki Okano
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Department of Physiology, Keio University School of Medicine, Tokyo 108-8345, Japan
| | - Shin Ishii
- Integrated Systems Biology Laboratory, Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Tetsuo Yamamori
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Laboratory for Haptic Perception and Cognitive Physiology, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan; Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821, Japan.
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Rapid 3D breath-hold MR cholangiopancreatography using deep learning-constrained compressed sensing reconstruction. Eur Radiol 2023; 33:2500-2509. [PMID: 36355200 DOI: 10.1007/s00330-022-09227-y] [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: 04/01/2022] [Revised: 08/15/2022] [Accepted: 10/09/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVES To compare the image quality of three-dimensional breath-hold magnetic resonance cholangiopancreatography with deep learning-based compressed sensing reconstruction (3D DL-CS-MRCP) to those of 3D breath-hold MRCP with compressed sensing (3D CS-MRCP), 3D breath-hold MRCP with gradient and spin-echo (3D GRASE-MRCP) and conventional 2D single-shot breath-hold MRCP (2D MRCP). METHODS In total, 102 consecutive patients who underwent MRCP at 3.0 T, including 2D MRCP, 3D GRASE-MRCP, 3D CS-MRCP, and 3D DL-CS-MRCP, were prospectively included. Two radiologists independently analyzed the overall image quality, background suppression, artifacts, and visualization of pancreaticobiliary ducts using a five-point scale. The signal-to-noise ratio (SNR) of the common bile duct (CBD), contrast-to-noise ratio (CNR) of the CBD and liver, and contrast ratio between the periductal tissue and CBD were measured. The Friedman test was performed to compare the four protocols. RESULTS 3D DL-CS-MRCP resulted in improved SNR and CNR values compared with those in the other three protocols, and better contrast ratio compared with that in 3D CS-MRCP and 3D GRASE-MRCP (all, p < 0.05). Qualitative image analysis showed that 3D DL-CS-MRCP had better performance for second-level intrahepatic ducts and distal main pancreatic ducts compared with 3D CS-MRCP (all, p < 0.05). Compared with 2D MRCP, 3D DL-CS-MRCP demonstrated better performance for the second-order left intrahepatic duct but was inferior in assessing the main pancreatic duct (all, p < 0.05). Moreover, the image quality was significantly higher in 3D DL-CS-MRCP than in 3D GRASE-MRCP. CONCLUSION 3D DL-CS-MRCP has superior performance compared with that of 3D CS-MRCP or 3D GRASE-MRCP. Deep learning reconstruction also provides a comparable image quality but with inferior main pancreatic duct compared with that revealed by 2D MRCP. KEY POINTS • 3D breath-hold MRCP with deep learning reconstruction (3D DL-CS-MRCP) demonstrated improved image quality compared with that of 3D MRCP with compressed sensing or GRASE. • Compared with 2D MRCP, 3D DL-CS-MRCP had superior performance in SNR and CNR, better visualization of the left second-level intrahepatic bile ducts, and comparable overall image quality, but an inferior main pancreatic duct.
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Faes LK, De Martino F, Huber L(R. Cerebral blood volume sensitive layer-fMRI in the human auditory cortex at 7T: Challenges and capabilities. PLoS One 2023; 18:e0280855. [PMID: 36758009 PMCID: PMC9910709 DOI: 10.1371/journal.pone.0280855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/09/2023] [Indexed: 02/10/2023] Open
Abstract
The development of ultra high field fMRI signal readout strategies and contrasts has led to the possibility of imaging the human brain in vivo and non-invasively at increasingly higher spatial resolutions of cortical layers and columns. One emergent layer-fMRI acquisition method with increasing popularity is the cerebral blood volume sensitive sequence named vascular space occupancy (VASO). This approach has been shown to be mostly sensitive to locally-specific changes of laminar microvasculature, without unwanted biases of trans-laminar draining veins. Until now, however, VASO has not been applied in the technically challenging cortical area of the auditory cortex. Here, we describe the main challenges we encountered when developing a VASO protocol for auditory neuroscientific applications and the solutions we have adopted. With the resulting protocol, we present preliminary results of laminar responses to sounds and as a proof of concept for future investigations, we map the topographic representation of frequency preference (tonotopy) in the auditory cortex.
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Affiliation(s)
- Lonike K. Faes
- Faculty of Psychology and Neuroscience, Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands
- * E-mail:
| | - Federico De Martino
- Faculty of Psychology and Neuroscience, Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Laurentius (Renzo) Huber
- Faculty of Psychology and Neuroscience, Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands
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7
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Demirayak P, Deshpande G, Visscher K. Laminar functional magnetic resonance imaging in vision research. Front Neurosci 2022; 16:910443. [PMID: 36267240 PMCID: PMC9577024 DOI: 10.3389/fnins.2022.910443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Magnetic resonance imaging (MRI) scanners at ultra-high magnetic fields have become available to use in humans, thus enabling researchers to investigate the human brain in detail. By increasing the spatial resolution, ultra-high field MR allows both structural and functional characterization of cortical layers. Techniques that can differentiate cortical layers, such as histological studies and electrode-based measurements have made critical contributions to the understanding of brain function, but these techniques are invasive and thus mainly available in animal models. There are likely to be differences in the organization of circuits between humans and even our closest evolutionary neighbors. Thus research on the human brain is essential. Ultra-high field MRI can observe differences between cortical layers, but is non-invasive and can be used in humans. Extensive previous literature has shown that neuronal connections between brain areas that transmit feedback and feedforward information terminate in different layers of the cortex. Layer-specific functional MRI (fMRI) allows the identification of layer-specific hemodynamic responses, distinguishing feedback and feedforward pathways. This capability has been particularly important for understanding visual processing, as it has allowed researchers to test hypotheses concerning feedback and feedforward information in visual cortical areas. In this review, we provide a general overview of successful ultra-high field MRI applications in vision research as examples of future research.
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Affiliation(s)
- Pinar Demirayak
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Pinar Demirayak,
| | - Gopikrishna Deshpande
- Department of Electrical and Computer Engineering, AU MRI Research Center, Auburn University, Auburn, AL, United States
- Department of Psychological Sciences, Auburn University, Auburn, AL, United States
- Alabama Advanced Imaging Consortium, Birmingham, AL, United States
- Center for Neuroscience, Auburn University, Auburn, AL, United States
- School of Psychology, Capital Normal University, Beijing, China
- Key Laboratory of Learning and Cognition, Capital Normal University, Beijing, China
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
- Centre for Brain Research, Indian Institute of Science, Bangalore, India
| | - Kristina Visscher
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
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Shao X, Guo F, Shou Q, Wang K, Jann K, Yan L, Toga AW, Zhang P, Wang DJJ. Laminar perfusion imaging with zoomed arterial spin labeling at 7 Tesla. Neuroimage 2021; 245:118724. [PMID: 34780918 PMCID: PMC8727512 DOI: 10.1016/j.neuroimage.2021.118724] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/23/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022] Open
Abstract
Laminar fMRI based on BOLD and CBV contrast at ultrahigh magnetic fields has been applied for studying the dynamics of mesoscopic brain networks. However, the quantitative interpretations of BOLD/CBV fMRI results are confounded by different baseline physiology across cortical layers. Here we introduce a novel 3D zoomed pseudo-continuous arterial spin labeling (pCASL) technique at 7T that offers the capability for quantitative measurements of laminar cerebral blood flow (CBF) both at rest and during task activation with high spatial specificity and sensitivity. We found arterial transit time in superficial layers is ∼100 ms shorter than in middle/deep layers revealing the time course of labeled blood flowing from pial arteries to downstream microvasculature. Resting state CBF peaked in the middle layers which is highly consistent with microvascular density measured from human cortex specimens. Finger tapping induced a robust two-peak laminar profile of CBF increases in the superficial (somatosensory and premotor input) and deep (spinal output) layers of M1, while finger brushing task induced a weaker CBF increase in superficial layers (somatosensory input). This observation is highly consistent with reported laminar profiles of CBV activation on M1. We further demonstrated that visuospatial attention induced a predominant CBF increase in deep layers and a smaller CBF increase on top of the lower baseline CBF in superficial layers of V1 (feedback cortical input), while stimulus driven activity peaked in the middle layers (feedforward thalamic input). With the capability for quantitative CBF measurements both at baseline and during task activation, high-resolution ASL perfusion fMRI at 7T provides an important tool for in vivo assessment of neurovascular function and metabolic activities of neural circuits across cortical layers.
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Affiliation(s)
- Xingfeng Shao
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA
| | - Fanhua Guo
- State Key Laboratory of Brain and Cognitive Science, Beijing MRI Center for Brain Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinyang Shou
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA
| | - Kai Wang
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA
| | - Kay Jann
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lirong Yan
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Peng Zhang
- State Key Laboratory of Brain and Cognitive Science, Beijing MRI Center for Brain Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Danny J J Wang
- Laboratory of FMRI Technology (LOFT), USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, 2025 Zonal Ave, Los Angeles, CA 90033, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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9
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Elam JS, Glasser MF, Harms MP, Sotiropoulos SN, Andersson JLR, Burgess GC, Curtiss SW, Oostenveld R, Larson-Prior LJ, Schoffelen JM, Hodge MR, Cler EA, Marcus DM, Barch DM, Yacoub E, Smith SM, Ugurbil K, Van Essen DC. The Human Connectome Project: A retrospective. Neuroimage 2021; 244:118543. [PMID: 34508893 PMCID: PMC9387634 DOI: 10.1016/j.neuroimage.2021.118543] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 01/21/2023] Open
Abstract
The Human Connectome Project (HCP) was launched in 2010 as an ambitious effort to accelerate advances in human neuroimaging, particularly for measures of brain connectivity; apply these advances to study a large number of healthy young adults; and freely share the data and tools with the scientific community. NIH awarded grants to two consortia; this retrospective focuses on the "WU-Minn-Ox" HCP consortium centered at Washington University, the University of Minnesota, and University of Oxford. In just over 6 years, the WU-Minn-Ox consortium succeeded in its core objectives by: 1) improving MR scanner hardware, pulse sequence design, and image reconstruction methods, 2) acquiring and analyzing multimodal MRI and MEG data of unprecedented quality together with behavioral measures from more than 1100 HCP participants, and 3) freely sharing the data (via the ConnectomeDB database) and associated analysis and visualization tools. To date, more than 27 Petabytes of data have been shared, and 1538 papers acknowledging HCP data use have been published. The "HCP-style" neuroimaging paradigm has emerged as a set of best-practice strategies for optimizing data acquisition and analysis. This article reviews the history of the HCP, including comments on key events and decisions associated with major project components. We discuss several scientific advances using HCP data, including improved cortical parcellations, analyses of connectivity based on functional and diffusion MRI, and analyses of brain-behavior relationships. We also touch upon our efforts to develop and share a variety of associated data processing and analysis tools along with detailed documentation, tutorials, and an educational course to train the next generation of neuroimagers. We conclude with a look forward at opportunities and challenges facing the human neuroimaging field from the perspective of the HCP consortium.
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Affiliation(s)
| | | | - Michael P Harms
- Washington University School of Medicine, St. Louis, MO, USA
| | - Stamatios N Sotiropoulos
- Sir Peter Mansfield Imaging Centre & NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, School of Medicine, University of Nottingham, UK; Wellcome Centre for Integrative Neuroimaging, University of Oxford, UK
| | | | | | | | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, the Netherlands
| | | | - Jan-Mathijs Schoffelen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, the Netherlands
| | - Michael R Hodge
- Washington University School of Medicine, St. Louis, MO, USA
| | - Eileen A Cler
- Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Marcus
- Washington University School of Medicine, St. Louis, MO, USA
| | - Deanna M Barch
- Washington University School of Medicine, St. Louis, MO, USA
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, UK
| | - Kamil Ugurbil
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
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10
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Wang F, Dong Z, Wald LL, Polimeni JR, Setsompop K. Simultaneous pure T 2 and varying T 2'-weighted BOLD fMRI using Echo Planar Time-resolved Imaging for mapping cortical-depth dependent responses. Neuroimage 2021; 245:118641. [PMID: 34655771 PMCID: PMC8820652 DOI: 10.1016/j.neuroimage.2021.118641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
Spin-echo (SE) BOLD fMRI has high microvascular specificity, and thus provides a more reliable means to localize neural activity compared to conventional gradient-echo BOLD fMRI. However, the most common SE BOLD acquisition method, SE-EPI, is known to suffer from T2′ contrast contamination with undesirable draining vein bias. To address this, in this study, we extended a recently developed distortion/blurring-free multi-shot EPI technique, Echo-Planar Time-resolved Imaging (EPTI), to cortical-depth dependent SE-fMRI at 7T to test whether it could provide purer SE BOLD contrast with minimal T2′ contamination for improved neuronal specificity. From the same acquisition, the time-resolved feature of EPTI also provides a series of asymmetric SE (ASE) images with varying T2′ weightings, and enables extraction of data equivalent to conventional SE EPI with different echo train lengths (ETLs). This allows us to systematically examine how T2′-contribution affects different SE acquisition strategies using a single dataset. A low-rank spatiotemporal subspace reconstruction was implemented for the SE-EPTI acquisition, which incorporates corrections for both shot-to-shot phase variations and dynamic B0 drifts. SE-EPTI was used in a visual task fMRI experiment to demonstrate that i) the pure SE image provided by EPTI results in the highest microvascular specificity; ii) the ASE EPTI series, with a graded introduction of T2′ weightings at time points farther away from the pure SE, show a gradual sensitivity increase along with increasing draining vein bias; iii) the longer ETL seen in conventional SE EPI acquisitions will induce more draining vein bias. Consistent results were observed across multiple subjects, demonstrating the robustness of the proposed technique for SE-BOLD fMRI with high specificity.
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Affiliation(s)
- Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA.
| | - Zijing Dong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Kawin Setsompop
- Department of Radiology, Stanford University, Stanford, USA; Department of Electrical Engineering, Stanford University, Stanford, USA
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11
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Scheffler K, Engelmann J, Heule R. BOLD sensitivity and vessel size specificity along CPMG and GRASE echo trains. Magn Reson Med 2021; 86:2076-2083. [PMID: 34056746 DOI: 10.1002/mrm.28871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
PURPOSE To assess the vessel size specificity and sensitivity of rapid CPMG and GRASE for functional BOLD imaging for different echo train lengths, echo spacings, field strength, and refocusing flip angle schemes. In addition, the behavior of signals acquired before and after the refocusing time points is analyzed. METHODS Evolution of magnetization within a network of artificial cylinders is simulated with Monte Carlo methods for all relevant coherence pathways. In addition, measurements on microspheres were performed to confirm some of the theoretical results. RESULTS For reduced refocusing flip angles, the peak of the vessel size sensitivity curve is shifting toward larger radii with increasing echo time. Furthermore, the BOLD-related signal change along the echo train depends on the chosen refocusing flip angle scheme and in general does not follow corresponding echo amplitudes. CONCLUSION CPMG or GRASE can be used with low refocusing flip angles without significant loss of sensitivity to BOLD. The evolution of BOLD signal changes along the echo train can be used to design optimal k-space reordering schemes. Signals acquired before or after the spin echo time point show contributions from larger vessels similar to gradient echo sequences. Short echo spacing (time between refocusing pulses) suppresses gradient echo-related contributions from larger vessels, whereas the spin echo-related contribution from small vessels remains constant and is independent of the echo spacing.
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Affiliation(s)
- Klaus Scheffler
- High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
| | - Jörn Engelmann
- High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Rahel Heule
- High-Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany
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12
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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: 23] [Impact Index Per Article: 5.8] [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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