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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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Taso M, Alsop DC. Arterial Spin Labeling Perfusion Imaging. Magn Reson Imaging Clin N Am 2024; 32:63-72. [PMID: 38007283 DOI: 10.1016/j.mric.2023.08.005] [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] [Indexed: 11/27/2023]
Abstract
Noninvasive imaging of tissue perfusion is a valuable tool for both research and clinical applications. Arterial spin labeling (ASL) is a contrast-free perfusion imaging method that enables measuring and quantifying tissue blood flow using MR imaging. ASL uses radiofrequency and magnetic field gradient pulses to label arterial blood water, which then serves as an endogenous tracer. This review highlights the basic mechanism of ASL perfusion imaging, labeling strategies, and quantification. ASL has been widely used during the past 30 years for the study of normal brain function as well as in multiple neurovascular, neuro-oncological and degenerative pathologic conditions.
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Affiliation(s)
- Manuel Taso
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - David C Alsop
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
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Knudsen L, Bailey CJ, Blicher JU, Yang Y, Zhang P, Lund TE. Improved sensitivity and microvascular weighting of 3T laminar fMRI with GE-BOLD using NORDIC and phase regression. Neuroimage 2023; 271:120011. [PMID: 36914107 DOI: 10.1016/j.neuroimage.2023.120011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
INTRODUCTION Functional MRI with spatial resolution in the submillimeter domain enables measurements of activation across cortical layers in humans. This is valuable as different types of cortical computations, e.g., feedforward versus feedback related activity, take place in different cortical layers. Laminar fMRI studies have almost exclusively employed 7T scanners to overcome the reduced signal stability associated with small voxels. However, such systems are relatively rare and only a subset of those are clinically approved. In the present study, we examined if the feasibility of laminar fMRI at 3T could be improved by use of NORDIC denoising and phase regression. METHODS 5 healthy subjects were scanned on a Siemens MAGNETOM Prisma 3T scanner. To assess across-session reliability, each subject was scanned in 3-8 sessions on 3-4 consecutive days. A 3D gradient echo EPI (GE-EPI) sequence was used for BOLD acquisitions (voxel size 0.82 mm isotopic, TR = 2.2 s) using a block design finger tapping paradigm. NORDIC denoising was applied to the magnitude and phase time series to overcome limitations in temporal signal-to-noise ratio (tSNR) and the denoised phase time series were subsequently used to correct for large vein contamination through phase regression. RESULTS AND CONCLUSION NORDIC denoising resulted in tSNR values comparable to or higher than commonly observed at 7T. Layer-dependent activation profiles could thus be extracted robustly, within and across sessions, from regions of interest located in the hand knob of the primary motor cortex (M1). Phase regression led to substantially reduced superficial bias in obtained layer profiles, although residual macrovascular contribution remained. We believe the present results support an improved feasibility of laminar fMRI at 3T.
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Affiliation(s)
- Lasse Knudsen
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China.
| | - Christopher J Bailey
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China
| | - Jakob U Blicher
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark; Department of Neurology, Aalborg University Hospital, Aalborg, Denmark
| | - Yan Yang
- Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China; Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China
| | - Peng Zhang
- Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, PR China; Institute of Biophysics, Chinese Academy of Sciences, Beijing, PR China
| | - Torben E Lund
- Department of Clinical Medicine, Center of Functionally Integrative Neuroscience (CFIN), Aarhus University, Universitetsbyen 3, Aarhus C 8000, Denmark
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Taso M, Munsch F, Girard OM, Duhamel G, Alsop DC, Varma G. Fast-spin-echo versus rapid gradient-echo for 3D magnetization-prepared acquisitions: Application to inhomogeneous magnetization transfer. Magn Reson Med 2023; 89:550-564. [PMID: 36306334 PMCID: PMC10848167 DOI: 10.1002/mrm.29461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE To evaluate the benefits of fast spin echo (FSE) imaging over rapid gradient-echo (RAGE) for magnetization-prepared inhomogeneous magnetization transfer (ihMT) imaging. METHODS A 3D FSE sequence was modified to include an ihMT preparation (ihMT-FSE) with an optional CSF suppression based on an inversion-recovery (ihMT-FLAIR). After numeric simulations assessing SNR benefits of FSE and the potential impact of an additional inversion-recovery, ihMT-RAGE, ihMT-FSE, and ihMT-FLAIR sequences were compared in a group of six healthy volunteers, evaluating image quality, thermal, and physiological noise as well as quantification using an ihMT saturation (ihMTsat) approach. A preliminary exploration in the cervical spinal cord was also conducted in a group of three healthy volunteers. RESULTS Several fold improvements in thermal SNR were observed with ihMT-FSE in agreement with numerical simulations. However, we observed significantly higher physiological noise in ihMT-FSE compared to ihMT-RAGE that was mitigated in ihMT-FLAIR, which provided the best total SNR (+74% and +49% compared to ihMT-RAGE in the white and gray matter, P ≤ 0.004). IhMTsat quantification was successful in all cases with strong correlation between all sequences (r2 > 0.75). Early experiments showed potential for spinal cord imaging. CONCLUSIONS FSE generally offers higher SNR compared to gradient-echo based acquisitions for magnetization-prepared contrasts as illustrated here in the case of ihMT. However, physiological noise has a significant effect, but an inversion-recovery-based CSF suppression was shown to be efficient in mitigating effects of CSF motion.
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Affiliation(s)
- Manuel Taso
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Fanny Munsch
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | | | | | - David C. Alsop
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Gopal Varma
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
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Hernandez‐Garcia L, Aramendía‐Vidaurreta V, Bolar DS, Dai W, Fernández‐Seara MA, Guo J, Madhuranthakam AJ, Mutsaerts H, Petr J, Qin Q, Schollenberger J, Suzuki Y, Taso M, Thomas DL, van Osch MJP, Woods J, Zhao MY, Yan L, Wang Z, Zhao L, Okell TW. Recent Technical Developments in ASL: A Review of the State of the Art. Magn Reson Med 2022; 88:2021-2042. [PMID: 35983963 PMCID: PMC9420802 DOI: 10.1002/mrm.29381] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/31/2022] [Accepted: 06/18/2022] [Indexed: 12/11/2022]
Abstract
This review article provides an overview of a range of recent technical developments in advanced arterial spin labeling (ASL) methods that have been developed or adopted by the community since the publication of a previous ASL consensus paper by Alsop et al. It is part of a series of review/recommendation papers from the International Society for Magnetic Resonance in Medicine Perfusion Study Group. Here, we focus on advancements in readouts and trajectories, image reconstruction, noise reduction, partial volume correction, quantification of nonperfusion parameters, fMRI, fingerprinting, vessel selective ASL, angiography, deep learning, and ultrahigh field ASL. We aim to provide a high level of understanding of these new approaches and some guidance for their implementation, with the goal of facilitating the adoption of such advances by research groups and by MRI vendors. Topics outside the scope of this article that are reviewed at length in separate articles include velocity selective ASL, multiple-timepoint ASL, body ASL, and clinical ASL recommendations.
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Affiliation(s)
| | | | - Divya S. Bolar
- Center for Functional Magnetic Resonance Imaging, Department of RadiologyUniversity of California at San DiegoSan DiegoCaliforniaUSA
| | - Weiying Dai
- Department of Computer ScienceState University of New York at BinghamtonBinghamtonNYUSA
| | | | - Jia Guo
- Department of BioengineeringUniversity of California RiversideRiversideCaliforniaUSA
| | | | - Henk Mutsaerts
- Department of Radiology & Nuclear MedicineAmsterdam University Medical Center, Amsterdam NeuroscienceAmsterdamThe Netherlands
| | - Jan Petr
- Helmholtz‐Zentrum Dresden‐RossendorfInstitute of Radiopharmaceutical Cancer ResearchDresdenGermany
| | - Qin Qin
- The Russell H. Morgan Department of Radiology and Radiological ScienceJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - Yuriko Suzuki
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUnited Kingdom
| | - Manuel Taso
- Division of MRI research, RadiologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - David L. Thomas
- Department of Brain Repair and RehabilitationUCL Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Matthias J. P. van Osch
- C.J. Gorter Center for high field MRI, Department of RadiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Joseph Woods
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUnited Kingdom
- Department of RadiologyUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Moss Y. Zhao
- Department of RadiologyStanford UniversityStanfordCaliforniaUSA
| | - Lirong Yan
- Department of Radiology, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Ze Wang
- Department of Diagnostic Radiology and Nuclear MedicineUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Li Zhao
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument ScienceZhejiang UniversityZhejiangPeople's Republic of China
| | - Thomas W. Okell
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUnited Kingdom
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Taso M, Munsch F, Alsop DC. The Boston ASL Template and Simulator: Initial development and implementation. J Neuroimaging 2022; 32:1080-1089. [PMID: 36045507 DOI: 10.1111/jon.13042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE Templates are a hallmark of image analysis in neuroimaging. However, while numerous structural templates exist and have facilitated single-subject and large group studies, templates based on functional contrasts, such as arterial spin labeling (ASL) perfusion, are scarce, have an inherently low spatial resolution, and are not as widely distributed. Having such tools at one's disposal is desirable, for example, in the case of studies not acquiring structural scans. We here propose an initial development of an ASL adult template based on high-resolution fast spin echo acquisitions. METHODS High-resolution single-delay ASL, low-resolution multi-delay ASL, T1 -weighted magnetization prepared rapid acquisition 2 gradient echoes, and T2 fluid attenuated inversion recovery data were acquired in a cohort of 10 healthy volunteers (6 males and 4 females, 30± 7 years old). After offline reconstruction of high-resolution perfusion arterial transit time (ATT) and T1 maps, we built a multi-contrast template relying on the Advanced Normalization Toolbox multivariate template nonlinear construction framework. We offer examples for the registration of ASL data acquired with different sequences. Finally, we propose an ASL simulator based on our templates and a standard kinetic model that allows generating synthetic ASL contrasts based on user-specified parameters. RESULTS Boston ASL Template and Simulator (BATS) offers high-quality, high-resolution perfusion-weighted and quantitative perfusion templates accompanied by ATT and different anatomical contrasts readily available in the Montreal Neurological Institute space. In addition, examples of use for data registration and as a synthetic contrast generator show various applications in which BATS could be used. CONCLUSIONS We propose a new ASL template collection, named BATS, that also includes a simulator allowing the generation of synthetic ASL contrasts. BATS is available at http://github.com/manueltaso/batsasltemplate.
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Affiliation(s)
- Manuel Taso
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Fanny Munsch
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - David C Alsop
- Division of MRI Research, Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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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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