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Jiang Y, Pais-Roldán P, Pohmann R, Yu X. High Spatiotemporal Resolution Radial Encoding Single-Vessel fMRI. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309218. [PMID: 38689514 DOI: 10.1002/advs.202309218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/23/2024] [Indexed: 05/02/2024]
Abstract
High-field preclinical functional MRI (fMRI) is enabled the high spatial resolution mapping of vessel-specific hemodynamic responses, that is single-vessel fMRI. In contrast to investigating the neuronal sources of the fMRI signal, single-vessel fMRI focuses on elucidating its vascular origin, which can be readily implemented to identify vascular changes relevant to vascular dementia or cognitive impairment. However, the limited spatial and temporal resolution of fMRI is hindered hemodynamic mapping of intracortical microvessels. Here, the radial encoding MRI scheme is implemented to measure BOLD signals of individual vessels penetrating the rat somatosensory cortex. Radial encoding MRI is employed to map cortical activation with a focal field of view (FOV), allowing vessel-specific functional mapping with 50 × 50 µm2 in-plane resolution at a 1 to 2 Hz sampling rate. Besides detecting refined hemodynamic responses of intracortical micro-venules, the radial encoding-based single-vessel fMRI enables the distinction of fMRI signals from vessel and peri-vessel voxels due to the different contribution of intravascular and extravascular effects.
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Affiliation(s)
- Yuanyuan Jiang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Patricia Pais-Roldán
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Rolf Pohmann
- High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, 72076, Tübingen, Germany
| | - Xin Yu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
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2
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Hike D, Liu X, Xie Z, Zhang B, Choi S, Zhou XA, Liu A, Murstein A, Jiang Y, Devor A, Yu X. High-resolution awake mouse fMRI at 14 Tesla. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570803. [PMID: 38106227 PMCID: PMC10723470 DOI: 10.1101/2023.12.08.570803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
High-resolution awake mouse fMRI remains challenging despite extensive efforts to address motion-induced artifacts and stress. This study introduces an implantable radiofrequency (RF) surface coil design that minimizes image distortion caused by the air/tissue interface of mouse brains while simultaneously serving as a headpost for fixation during scanning. Using a 14T scanner, high-resolution fMRI enabled brain-wide functional mapping of visual and vibrissa stimulation at 100×100×200μm resolution with a 2s per frame sampling rate. Besides activated ascending visual and vibrissa pathways, robust BOLD responses were detected in the anterior cingulate cortex upon visual stimulation and spread through the ventral retrosplenial area (VRA) with vibrissa air-puff stimulation, demonstrating higher-order sensory processing in association cortices of awake mice. In particular, the rapid hemodynamic responses in VRA upon vibrissa stimulation showed a strong correlation with the hippocampus, thalamus, and prefrontal cortical areas. Cross-correlation analysis with designated VRA responses revealed early positive BOLD signals at the contralateral barrel cortex (BC) occurring 2 seconds prior to the air-puff in awake mice with repetitive stimulation, which was not detectable with the randomized stimulation paradigm. This early BC activation indicated learned anticipation through the vibrissa system and association cortices in awake mice under continuous training of repetitive air-puff stimulation. This work establishes a high-resolution awake mouse fMRI platform, enabling brain-wide functional mapping of sensory signal processing in higher association cortical areas.
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Affiliation(s)
- David Hike
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Xiaochen Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Zeping Xie
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Bei Zhang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Sangcheon Choi
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Xiaoqing Alice Zhou
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Andy Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
- Graduate program in Neuroscience, Boston University, Commonwealth Ave, Boston, Massachusetts, USA, 02215
| | - Alyssa Murstein
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
- Graduate program in Neuroscience, Boston University, Commonwealth Ave, Boston, Massachusetts, USA, 02215
| | - Yuanyuan Jiang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
| | - Anna Devor
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
- Department of Biomedical Engineering, Boston University, 610 Commonwealth Avenue, Boston, Massachusetts, USA, 02215
| | - Xin Yu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 Thirteenth Street, Charlestown, Massachusetts, USA 02129
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3
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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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4
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Li B, Li N, Wang Z, Balan R, Ernst T. Simultaneous multislice EPI prospective motion correction by real-time receiver phase correction and coil sensitivity map interpolation. Magn Reson Med 2023; 90:1932-1948. [PMID: 37448116 PMCID: PMC10795703 DOI: 10.1002/mrm.29789] [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: 09/29/2022] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
PURPOSE To improve the image reconstruction for prospective motion correction (PMC) of simultaneous multislice (SMS) EPI of the brain, an update of receiver phase and resampling of coil sensitivities are proposed and evaluated. METHODS A camera-based system was used to track head motion (3 translations and 3 rotations) and dynamically update the scan position and orientation. We derived the change in receiver phase associated with a shifted field of view (FOV) and applied it in real-time to each k-space line of the EPI readout trains. Second, for the SMS reconstruction, we adapted resampled coil sensitivity profiles reflecting the movement of slices. Single-shot gradient-echo SMS-EPI scans were performed in phantoms and human subjects for validation. RESULTS Brain SMS-EPI scans in the presence of motion with PMC and no phase correction for scan plane shift showed noticeable artifacts. These artifacts were visually and quantitatively attenuated when corrections were enabled. Correcting misaligned coil sensitivity maps improved the temporal SNR (tSNR) of time series by 24% (p = 0.0007) for scans with large movements (up to ˜35 mm and 30°). Correcting the receiver phase improved the tSNR of a scan with minimal head movement by 50% from 50 to 75 for a United Kingdom biobank protocol. CONCLUSION Reconstruction-induced motion artifacts in single-shot SMS-EPI scans acquired with PMC can be removed by dynamically adjusting the receiver phase of each line across EPI readout trains and updating coil sensitivity profiles during reconstruction. The method may be a valuable tool for SMS-EPI scans in the presence of subject motion.
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Affiliation(s)
- Bo Li
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, MD, United States
| | - Ningzhi Li
- U.S. Food Drug Administration, Silver Spring, MD, United States
| | - Ze Wang
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, MD, United States
| | - Radu Balan
- Department of Mathematics, University of Maryland, College Park, MD, United States
| | - Thomas Ernst
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, MD, United States
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5
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Priovoulos N, de Oliveira IAF, Poser BA, Norris DG, van der Zwaag W. Combining arterial blood contrast with BOLD increases fMRI intracortical contrast. Hum Brain Mapp 2023; 44:2509-2522. [PMID: 36763562 PMCID: PMC10028680 DOI: 10.1002/hbm.26227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
BOLD fMRI is widely applied in human neuroscience but is limited in its spatial specificity due to a cortical-depth-dependent venous bias. This reduces its localization specificity with respect to neuronal responses, a disadvantage for neuroscientific research. Here, we modified a submillimeter BOLD protocol to selectively reduce venous and tissue signal and increase cerebral blood volume weighting through a pulsed saturation scheme (dubbed Arterial Blood Contrast) at 7 T. Adding Arterial Blood Contrast on top of the existing BOLD contrast modulated the intracortical contrast. Isolating the Arterial Blood Contrast showed a response free of pial-surface bias. The results suggest that Arterial Blood Contrast can modulate the typical fMRI spatial specificity, with important applications in in-vivo neuroscience.
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Affiliation(s)
- Nikos Priovoulos
- Spinoza Center for Neuroimaging, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Computational Cognitive Neuroscience and Neuroimaging, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Icaro Agenor Ferreira de Oliveira
- Spinoza Center for Neuroimaging, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Computational Cognitive Neuroscience and Neuroimaging, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
- Experimental and Applied Psychology, VU University, Amsterdam, The Netherlands
| | - Benedikt A Poser
- MR-Methods Group, Maastricht Brain Imaging Center, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - David G Norris
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
- Erwin L. Hahn Institute for MRI, University of Duisburg-Essen, Essen, Germany
| | - Wietske van der Zwaag
- Spinoza Center for Neuroimaging, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Computational Cognitive Neuroscience and Neuroimaging, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
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6
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Davids M, Dietz P, Ruyters G, Roesler M, Klein V, Guérin B, Feinberg DA, Wald LL. Peripheral nerve stimulation informed design of a high-performance asymmetric head gradient coil. Magn Reson Med 2023; 90:784-801. [PMID: 37052387 DOI: 10.1002/mrm.29668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 04/14/2023]
Abstract
PURPOSE Peripheral nerve stimulation (PNS) limits the image encoding performance of both body gradient coils and the latest generation of head gradients. We analyze a variety of head gradient design aspects using a detailed PNS model to guide the design process of a new high-performance asymmetric head gradient to raise PNS thresholds and maximize the usable image-encoding performance. METHODS A novel three-layer coil design underwent PNS optimization involving PNS predictions of a series of candidate designs. The PNS-informed design process sought to maximize the usable parameter space of a coil with <10% nonlinearity in a 22 cm region of linearity, a relatively large inner diameter (44 cm), maximum gradient amplitude of 200 mT/m, and a high slew rate of 900 T/m/s. PNS modeling allowed identification and iterative adjustment of coil features with beneficial impact on PNS such as the number of winding layers, shoulder accommodation strategy, and level of asymmetry. PNS predictions for the final design were compared to measured thresholds in a constructed prototype. RESULTS The final head gradient achieved up to 2-fold higher PNS thresholds than the initial design without PNS optimization and compared to existing head gradients with similar design characteristics. The inclusion of a third intermediate winding layer provided the additional degrees of freedom necessary to improve PNS thresholds without significant sacrifices to the other design metrics. CONCLUSION Augmenting the design phase of a new high-performance head gradient coil by PNS modeling dramatically improved the usable image-encoding performance by raising PNS thresholds.
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Affiliation(s)
- Mathias Davids
- A.A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Valerie Klein
- A.A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Bastien Guérin
- A.A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - David A Feinberg
- Advanced MRI Technologies, Sebastopol, California, USA
- Brain Imaging Center and Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - Lawrence L Wald
- A.A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences Technology, Cambridge, Massachusetts, USA
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7
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Feature-space selection with banded ridge regression. Neuroimage 2022; 264:119728. [PMID: 36334814 PMCID: PMC9807218 DOI: 10.1016/j.neuroimage.2022.119728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Encoding models provide a powerful framework to identify the information represented in brain recordings. In this framework, a stimulus representation is expressed within a feature space and is used in a regularized linear regression to predict brain activity. To account for a potential complementarity of different feature spaces, a joint model is fit on multiple feature spaces simultaneously. To adapt regularization strength to each feature space, ridge regression is extended to banded ridge regression, which optimizes a different regularization hyperparameter per feature space. The present paper proposes a method to decompose over feature spaces the variance explained by a banded ridge regression model. It also describes how banded ridge regression performs a feature-space selection, effectively ignoring non-predictive and redundant feature spaces. This feature-space selection leads to better prediction accuracy and to better interpretability. Banded ridge regression is then mathematically linked to a number of other regression methods with similar feature-space selection mechanisms. Finally, several methods are proposed to address the computational challenge of fitting banded ridge regressions on large numbers of voxels and feature spaces. All implementations are released in an open-source Python package called Himalaya.
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8
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Pais-Roldán P, Yun SD, Shah NJ. Pre-processing of Sub-millimeter GE-BOLD fMRI Data for Laminar Applications. FRONTIERS IN NEUROIMAGING 2022; 1:869454. [PMID: 37555171 PMCID: PMC10406219 DOI: 10.3389/fnimg.2022.869454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/31/2022] [Indexed: 08/10/2023]
Abstract
Over the past 30 years, brain function has primarily been evaluated non-invasively using functional magnetic resonance imaging (fMRI) with gradient-echo (GE) sequences to measure blood-oxygen-level-dependent (BOLD) signals. Despite the multiple advantages of GE sequences, e.g., higher signal-to-noise ratio, faster acquisitions, etc., their relatively inferior spatial localization compromises the routine use of GE-BOLD in laminar applications. Here, in an attempt to rescue the benefits of GE sequences, we evaluated the effect of existing pre-processing methods on the spatial localization of signals obtained with EPIK, a GE sequence that affords voxel volumes of 0.25 mm3 with near whole-brain coverage. The methods assessed here apply to both task and resting-state fMRI data assuming the availability of reconstructed magnitude and phase images.
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Affiliation(s)
- Patricia Pais-Roldán
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Seong Dae Yun
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - N. Jon Shah
- Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11, Molecular Neuroscience and Neuroimaging, Jülich Aachen Research Alliance, Forschungszentrum Jülich, Jülich, Germany
- Jlich Aachen Research Alliance, Brain - Translational Medicine, Aachen, Germany
- Department of Neurology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
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9
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Yun SD, Pais-Roldán P, Palomero-Gallagher N, Shah NJ. Mapping of whole-cerebrum resting-state networks using ultra-high resolution acquisition protocols. Hum Brain Mapp 2022; 43:3386-3403. [PMID: 35384130 PMCID: PMC9248311 DOI: 10.1002/hbm.25855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 12/28/2022] Open
Abstract
Resting‐state functional magnetic resonance imaging (fMRI) has been used in numerous studies to map networks in the brain that employ spatially disparate regions. However, attempts to map networks with high spatial resolution have been hampered by conflicting technical demands and associated problems. Results from recent fMRI studies have shown that spatial resolution remains around 0.7 × 0.7 × 0.7 mm3, with only partial brain coverage. Therefore, this work aims to present a novel fMRI technique that was developed based on echo‐planar‐imaging with keyhole (EPIK) combined with repetition‐time‐external (TR‐external) EPI phase correction. Each technique has been previously shown to be effective in enhancing the spatial resolution of fMRI, and in this work, the combination of the two techniques into TR‐external EPIK provided a nominal spatial resolution of 0.51 × 0.51 × 1.00 mm3 (0.26 mm3 voxel) with whole‐cerebrum coverage. Here, the feasibility of using half‐millimetre in‐plane TR‐external EPIK for resting‐state fMRI was validated using 13 healthy subjects and the corresponding reproducible mapping of resting‐state networks was demonstrated. Furthermore, TR‐external EPIK enabled the identification of various resting‐state networks distributed throughout the brain from a single fMRI session, with mapping fidelity onto the grey matter at 7T. The high‐resolution functional image further revealed mesoscale anatomical structures, such as small cerebral vessels and the internal granular layer of the cortex within the postcentral gyrus.
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Affiliation(s)
- Seong Dae Yun
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Patricia Pais-Roldán
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany
| | - Nicola Palomero-Gallagher
- Institute of Neuroscience and Medicine-1, Structural and Functional Organisation of the Brain, Forschungszentrum Jülich, Jülich, Germany.,C. & O. Vogt Institute for Brain Research, Heinrich-Heine-University, Düsseldorf, Germany.,Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen, Aachen, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine-4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany.,Institute of Neuroscience and Medicine-11, Molecular Neuroscience and Neuroimaging, JARA, Forschungszentrum Jülich, Jülich, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Department of Neurology, RWTH Aachen University, Aachen, Germany
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10
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Advances in spiral fMRI: A high-resolution study with single-shot acquisition. Neuroimage 2021; 246:118738. [PMID: 34800666 DOI: 10.1016/j.neuroimage.2021.118738] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 01/15/2023] Open
Abstract
Spiral fMRI has been put forward as a viable alternative to rectilinear echo-planar imaging, in particular due to its enhanced average k-space speed and thus high acquisition efficiency. This renders spirals attractive for contemporary fMRI applications that require high spatiotemporal resolution, such as laminar or columnar fMRI. However, in practice, spiral fMRI is typically hampered by its reduced robustness and ensuing blurring artifacts, which arise from imperfections in both static and dynamic magnetic fields. Recently, these limitations have been overcome by the concerted application of an expanded signal model that accounts for such field imperfections, and its inversion by iterative image reconstruction. In the challenging ultra-high field environment of 7 Tesla, where field inhomogeneity effects are aggravated, both multi-shot and single-shot 2D spiral imaging at sub-millimeter resolution was demonstrated with high depiction quality and anatomical congruency. In this work, we further these advances towards a time series application of spiral readouts, namely, single-shot spiral BOLD fMRI at 0.8 mm in-plane resolution. We demonstrate that high-resolution spiral fMRI at 7 T is not only feasible, but delivers both excellent image quality, BOLD sensitivity, and spatial specificity of the activation maps, with little artifactual blurring. Furthermore, we show the versatility of the approach with a combined in/out spiral readout at a more typical resolution (1.5 mm), where the high acquisition efficiency allows to acquire two images per shot for improved sensitivity by echo combination.
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11
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Lee SH, Broadwater MA, Ban W, Wang TWW, Kim HJ, Dumas JS, Vetreno RP, Herman MA, Morrow AL, Besheer J, Kash TL, Boettiger CA, Robinson DL, Crews FT, Shih YYI. An isotropic EPI database and analytical pipelines for rat brain resting-state fMRI. Neuroimage 2021; 243:118541. [PMID: 34478824 PMCID: PMC8561231 DOI: 10.1016/j.neuroimage.2021.118541] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/08/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
Resting-state functional magnetic resonance imaging (fMRI) has drastically expanded the scope of brain research by advancing our knowledge about the topologies, dynamics, and interspecies translatability of functional brain networks. Several databases have been developed and shared in accordance with recent key initiatives in the rodent fMRI community to enhance the transparency, reproducibility, and interpretability of data acquired at various sites. Despite these pioneering efforts, one notable challenge preventing efficient standardization in the field is the customary choice of anisotropic echo planar imaging (EPI) schemes with limited spatial coverage. Imaging with anisotropic resolution and/or reduced brain coverage has significant shortcomings including reduced registration accuracy and increased deviation in brain feature detection. Here we proposed a high-spatial-resolution (0.4 mm), isotropic, whole-brain EPI protocol for the rat brain using a horizontal slicing scheme that can maintain a functionally relevant repetition time (TR), avoid high gradient duty cycles, and offer unequivocal whole-brain coverage. Using this protocol, we acquired resting-state EPI fMRI data from 87 healthy rats under the widely used dexmedetomidine sedation supplemented with low-dose isoflurane on a 9.4 T MRI system. We developed an EPI template that closely approximates the Paxinos and Watson's rat brain coordinate system and demonstrated its ability to improve the accuracy of group-level approaches and streamline fMRI data pre-processing. Using this database, we employed a multi-scale dictionary-learning approach to identify reliable spatiotemporal features representing rat brain intrinsic activity. Subsequently, we performed k-means clustering on those features to obtain spatially discrete, functional regions of interest (ROIs). Using Euclidean-based hierarchical clustering and modularity-based partitioning, we identified the topological organizations of the rat brain. Additionally, the identified group-level FC network appeared robust across strains and sexes. The "triple-network" commonly adapted in human fMRI were resembled in the rat brain. Through this work, we disseminate raw and pre-processed isotropic EPI data, a rat brain EPI template, as well as identified functional ROIs and networks in standardized rat brain coordinates. We also make our analytical pipelines and scripts publicly available, with the hope of facilitating rat brain resting-state fMRI study standardization.
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Affiliation(s)
- Sung-Ho Lee
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Corresponding authors at: Center for Animal MRI, 125 Mason Farm Road, CB# 7513, University of North Carolina, Chapel Hill, NC 27599, USA. (S.-H. Lee), (Y.-Y.I. Shih)
| | - Margaret A. Broadwater
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA
| | - Woomi Ban
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA
| | - Tzu-Wen Winnie Wang
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hyeon-Joong Kim
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA
| | - Jaiden Seongmi Dumas
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Department of Quantitative Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Ryan P. Vetreno
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Melissa A. Herman
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - A. Leslie Morrow
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Joyce Besheer
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas L. Kash
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Charlotte A. Boettiger
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
| | - Donita L. Robinson
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Fulton T. Crews
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Yen-Yu Ian Shih
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Corresponding authors at: Center for Animal MRI, 125 Mason Farm Road, CB# 7513, University of North Carolina, Chapel Hill, NC 27599, USA. (S.-H. Lee), (Y.-Y.I. Shih)
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Cheng PW, Chiueh TD, Chen JH. A high temporal/spatial resolution neuro-architecture study of rodent brain by wideband echo planar imaging. Sci Rep 2021; 11:20243. [PMID: 34642349 PMCID: PMC8511014 DOI: 10.1038/s41598-021-98132-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Latest simultaneous multi-slice (SMS) methods greatly benefit MR efficiency for recent studies using parallel imaging technique. However, these methods are limited by the requirement of array coils. The proposed Coherent Wideband method, which employs an extended field of view to separate multiple excited slices, can be applied to any existing MRI instrument, even those without array coils. In this study, the Coherent Wideband echo-planar imaging method was implemented on 7 T animal MRI to exhibit comprehensive enhancements in neuro-architecture, including diffusion tensor imaging (DTI) and functional MR studies (fMRI). Under the same scan time, the time-saving effect can be manipulated to increase the number of averages for DTI SNR improvement, reducing fractional anisotropy difference by 56.9% (from 0.072 to 0.041) and the deviation angle by 64% (from 25.3° to 16.2°). In summary, Coherent Wideband Echo Planar Imaging (EPI) will provide faster, higher resolution, thinner slice, or higher SNR imaging for precision neuro-architecture studies.
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Affiliation(s)
- Po-Wei Cheng
- Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Tzi-Dar Chiueh
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
| | - Jyh-Horng Chen
- Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taipei, Taiwan.
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
- Department of Electrical Engineering, Interdisciplinary MRI/MRS Lab, National Taiwan University, Taipei, Taiwan.
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Versteeg E, van der Velden TA, van Leeuwen CC, Borgo M, Huijing ER, Hendriks AD, Hendrikse J, Klomp DWJ, Siero JCW. A plug-and-play, lightweight, single-axis gradient insert design for increasing spatiotemporal resolution in echo planar imaging-based brain imaging. NMR IN BIOMEDICINE 2021; 34:e4499. [PMID: 33619838 PMCID: PMC8244051 DOI: 10.1002/nbm.4499] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 05/25/2023]
Abstract
The goal of this study was to introduce and evaluate the performance of a lightweight, high-performance, single-axis (z-axis) gradient insert design primarily intended for high-resolution functional magnetic resonance imaging, and aimed at providing both ease of use and a boost in spatiotemporal resolution. The optimal winding positions of the coil were obtained using a genetic algorithm with a cost function that balanced gradient performance (minimum 0.30 mT/m/A) and field linearity (≥16 cm linear region). These parameters were verified using field distribution measurements by B0 -mapping. The correction of geometrical distortions was performed using theoretical field distribution of the coil. Simulations and measurements were performed to investigate the echo planar imaging echo-spacing reduction due to the improved gradient performance. The resulting coil featured a 16-cm linear region, a weight of 45 kg, an installation time of 15 min, and a maximum gradient strength and slew rate of 200 mT/m and 1300 T/m/s, respectively, when paired with a commercially available gradient amplifier (940 V/630 A). The field distribution measurements matched the theoretically expected field. By utilizing the theoretical field distribution, geometrical distortions were corrected to within 6% of the whole-body gradient reference image in the target region. Compared with a whole-body gradient set, a maximum reduction in echo-spacing of a factor of 2.3 was found, translating to a 344 μs echo-spacing, for a field of view of 192 mm, a receiver bandwidth of 920 kHz and a gradient amplitude of 112 mT/m. We present a lightweight, single-axis gradient insert design that can provide high gradient performance and an increase in spatiotemporal resolution with correctable geometrical distortions while also offering a short installation time of less than 15 min and minimal system modifications.
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Affiliation(s)
- Edwin Versteeg
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | | | | | - Erik R. Huijing
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Arjan D. Hendriks
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Jeroen Hendrikse
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Dennis W. J. Klomp
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Jeroen C. W. Siero
- Department of RadiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
- Spinoza Center for NeuroimagingAmsterdamthe Netherlands
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Stanley OW, Kuurstra AB, Klassen LM, Menon RS, Gati JS. Effects of phase regression on high-resolution functional MRI of the primary visual cortex. Neuroimage 2020; 227:117631. [PMID: 33316391 DOI: 10.1016/j.neuroimage.2020.117631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
High-resolution functional MRI studies have become a powerful tool to non-invasively probe the sub-millimeter functional organization of the human cortex. Advances in MR hardware, imaging techniques and sophisticated post-processing methods have allowed high resolution fMRI to be used in both the clinical and academic neurosciences. However, consensus within the community regarding the use of gradient echo (GE) or spin echo (SE) based acquisition remains largely divided. On one hand, GE provides a high temporal signal-to-noise ratio (tSNR) technique sensitive to both the macro- and micro-vascular signal while SE based methods are more specific to microvasculature but suffer from lower tSNR and specific absorption rate limitations, especially at high field and with short repetition times. Fortunately, the phase of the GE-EPI signal is sensitive to vessel size and this provides a potential avenue to reduce the macrovascular weighting of the signal (phase regression, Menon 2002). In order to determine the efficacy of this technique at high-resolution, phase regression was applied to GE-EPI timeseries and compared to SE-EPI to determine if GE-EPI's specificity to the microvascular compartment improved. To do this, functional data was collected from seven subjects on a neuro-optimized 7 T system at 800 μm isotropic resolution with both GE-EPI and SE-EPI while observing an 8 Hz contrast reversing checkerboard. Phase data from the GE-EPI was used to create a microvasculature-weighted time series (GE-EPI-PR). Anatomical imaging (MP2RAGE) was also collected to allow for surface segmentation so that the functional results could be projected onto a surface. A multi-echo gradient echo sequence was collected and used to identify venous vasculature. The GE-EPI-PR surface activation maps showed a high qualitative similarity with SE-EPI and also produced laminar activity profiles similar to SE-EPI. When the GE-EPI and GE-EPI-PR distributions were compared to SE-EPI it was shown that GE-EPI-PR had similar distribution characteristics to SE-EPI (p < 0.05) across the top 60% of cortex. Furthermore, it was shown that GE-EPI-PR has a higher contrast-to-noise ratio (0.5 ± 0.2, mean ± std. dev. across layers) than SE-EPI (0.27 ± 0.07) demonstrating the technique has higher sensitivity than SE-EPI. Taken together this evidence suggests phase regression is a useful method in low SNR studies such as high-resolution fMRI.
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Affiliation(s)
- Olivia W Stanley
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada.
| | - Alan B Kuurstra
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada
| | - L Martyn Klassen
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Ravi S Menon
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Joseph S Gati
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, The University of Western Ontario, London, Ontario, Canada; Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
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Bollmann S, Barth M. New acquisition techniques and their prospects for the achievable resolution of fMRI. Prog Neurobiol 2020; 207:101936. [PMID: 33130229 DOI: 10.1016/j.pneurobio.2020.101936] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/10/2020] [Accepted: 10/18/2020] [Indexed: 01/17/2023]
Abstract
This work reviews recent advances in technologies for functional magnetic resonance imaging (fMRI) of the human brain and highlights the push for higher functional specificity based on increased spatial resolution and specific MR contrasts to reveal previously undetectable functional properties of small-scale cortical structures. We discuss how the combination of MR hardware, advanced acquisition techniques and various MR contrast mechanisms have enabled recent progress in functional neuroimaging. However, these advanced fMRI practices have only been applied to a handful of neuroscience questions to date, with the majority of the neuroscience community still using conventional imaging techniques. We thus discuss upcoming challenges and possibilities for fMRI technology development in human neuroscience. We hope that readers interested in functional brain imaging acquire an understanding of current and novel developments and potential future applications, even if they don't have a background in MR physics or engineering. We summarize the capabilities of standard fMRI acquisition schemes with pointers to relevant literature and comprehensive reviews and introduce more recent developments.
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Affiliation(s)
- Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Markus Barth
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia; School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Australia; ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, QLD, Australia.
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17
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Layer-dependent functional connectivity methods. Prog Neurobiol 2020; 207:101835. [DOI: 10.1016/j.pneurobio.2020.101835] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/30/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022]
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18
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Hendriks AD, D'Agata F, Raimondo L, Schakel T, Geerts L, Luijten PR, Klomp DW, Petridou N. Pushing functional MRI spatial and temporal resolution further: High-density receive arrays combined with shot-selective 2D CAIPIRINHA for 3D echo-planar imaging at 7 T. NMR IN BIOMEDICINE 2020; 33:e4281. [PMID: 32128898 PMCID: PMC7187278 DOI: 10.1002/nbm.4281] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 05/04/2023]
Abstract
To be able to examine dynamic and detailed brain functions, the spatial and temporal resolution of 7 T MRI needs to improve. In this study, it was investigated whether submillimeter multishot 3D EPI fMRI scans, acquired with high-density receive arrays, can benefit from a 2D CAIPIRINHA sampling pattern, in terms of noise amplification (g-factor), temporal SNR and fMRI sensitivity. High-density receive arrays were combined with a shot-selective 2D CAIPIRINHA implementation for multishot 3D EPI sequences at 7 T. In this implementation, in contrast to conventional inclusion of extra kz gradient blips, specific EPI shots are left out to create a CAIPIRINHA shift and reduction of scan time. First, the implementation of the CAIPIRINHA sequence was evaluated with a standard receive setup by acquiring submillimeter whole brain T2 *-weighted anatomy images. Second, the CAIPIRINHA sequence was combined with high-density receive arrays to push the temporal resolution of submillimeter 3D EPI fMRI scans of the visual cortex. Results show that the shot-selective 2D CAIPIRINHA sequence enables a reduction in scan time for 0.5 mm isotropic 3D EPI T2 *-weighted anatomy scans by a factor of 4 compared with earlier reports. The use of the 2D CAIPIRINHA implementation in combination with high-density receive arrays, enhances the image quality of submillimeter 3D EPI scans of the visual cortex at high acceleration as compared to conventional SENSE. Both the g-factor and temporal SNR improved, resulting in a method that is more sensitive to the fMRI signal. Using this method, it is possible to acquire submillimeter single volume 3D EPI scans of the visual cortex in a subsecond timeframe. Overall, high-density receive arrays in combination with shot-selective 2D CAIPIRINHA for 3D EPI scans prove to be valuable for reducing the scan time of submillimeter MRI acquisitions.
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Affiliation(s)
- Arjan D. Hendriks
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | - Federico D'Agata
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
- Department of NeuroscienceUniversity of TurinTurinItaly
| | - Luisa Raimondo
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
- Spinoza Centre for NeuroimagingAmsterdamthe Netherlands
| | - Tim Schakel
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | | | - Peter R. Luijten
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | - Dennis W.J. Klomp
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | - Natalia Petridou
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
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Ahmadi K, Fracasso A, Puzniak RJ, Gouws AD, Yakupov R, Speck O, Kaufmann J, Pestilli F, Dumoulin SO, Morland AB, Hoffmann MB. Triple visual hemifield maps in a case of optic chiasm hypoplasia. Neuroimage 2020; 215:116822. [PMID: 32276070 DOI: 10.1016/j.neuroimage.2020.116822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/27/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022] Open
Abstract
In humans, each hemisphere comprises an overlay of two visuotopic maps of the contralateral visual field, one from each eye. Is the capacity of the visual cortex limited to these two maps or are plastic mechanisms available to host more maps? We determined the cortical organization of the visual field maps in a rare individual with chiasma hypoplasia, where visual cortex plasticity is challenged to accommodate three hemifield maps. Using high-resolution fMRI at 7T and diffusion-weighted MRI at 3T, we found three hemiretinal inputs, instead of the normal two, to converge onto the left hemisphere. fMRI-based population receptive field mapping of the left V1-V3 at 3T revealed three superimposed hemifield representations in the left visual cortex, i.e. two representations of opposing visual hemifields from the left eye and one right hemifield representation from the right eye. We conclude that developmental plasticity including the re-wiring of local intra- and cortico-cortical connections is pivotal to support the coexistence and functioning of three hemifield maps within one hemisphere.
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Affiliation(s)
- Khazar Ahmadi
- Department of Ophthalmology, Otto-von-Guericke University, Magdeburg, 39120, Germany; Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, 22362, Sweden
| | - Alessio Fracasso
- Department of Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, 3584 CS, the Netherlands; Department of Radiology, University Medical Center Utrecht, Utrecht, 3584 CX, the Netherlands; Spinoza Centre for Neuroimaging, Amsterdam, 1105 BK, the Netherlands; Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, G12 8QB, UK
| | - Robert J Puzniak
- Department of Ophthalmology, Otto-von-Guericke University, Magdeburg, 39120, Germany
| | - Andre D Gouws
- Department of Psychology, York Neuroimaging Centre, University of York, York, YO10 5NY, UK
| | - Renat Yakupov
- Department of Biomedical Magnetic Resonance, Institute for Physics, Otto-von-Guericke University, Magdeburg, 39120, Germany; German Center for Neurodegenerative Diseases, Magdeburg, 39120, Germany
| | - Oliver Speck
- Department of Biomedical Magnetic Resonance, Institute for Physics, Otto-von-Guericke University, Magdeburg, 39120, Germany; German Center for Neurodegenerative Diseases, Magdeburg, 39120, Germany; Leibniz Institute for Neurobiology, Magdeburg, 39118, Germany; Center for Behavioral Brain Sciences, Magdeburg, 39106, Germany
| | - Joern Kaufmann
- Department of Neurology, Otto-von-Guericke-University, Magdeburg, 39120, Germany
| | - Franco Pestilli
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 1101 E, USA
| | - Serge O Dumoulin
- Department of Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, 3584 CS, the Netherlands; Spinoza Centre for Neuroimaging, Amsterdam, 1105 BK, the Netherlands; Department of Experimental and Applied Psychology, VU University Amsterdam, Amsterdam, 1081 BT, the Netherlands
| | - Antony B Morland
- Department of Psychology, York Neuroimaging Centre, University of York, York, YO10 5NY, UK; Centre for Neuroscience, Hull-York Medical School, University of York, York, YO10 5DD, UK
| | - Michael B Hoffmann
- Department of Ophthalmology, Otto-von-Guericke University, Magdeburg, 39120, Germany; Center for Behavioral Brain Sciences, Magdeburg, 39106, Germany.
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Hsu KJ, Lin YY, Lin YY, Su K, Feng KL, Wu SC, Lin YC, Chiang AS, Chu SW. Millisecond two-photon optical ribbon imaging for small-animal functional connectome study. OPTICS LETTERS 2019; 44:3190-3193. [PMID: 31259918 DOI: 10.1364/ol.44.003190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
We developed a high-speed two-photon optical ribbon imaging system, which combines galvo-mirrors for an arbitrary curve scan on a lateral plane and a tunable acoustic gradient-index lens for a 100 kHz-1 MHz axial scan. The system provides micrometer/millisecond spatiotemporal resolutions, which enable continuous readout of functional dynamics from small and densely packed neurons in a living adult Drosophila brain. Compared to sparse sampling techniques, the ribbon imaging modality avoids motion artifacts. Combined with a Drosophila anatomical connectome database, which is the most complete among all model animals, this technique paves the way toward establishing whole-brain functional connectome.
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22
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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: 1.8] [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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23
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Fast imaging for mapping dynamic networks. Neuroimage 2018; 180:547-558. [DOI: 10.1016/j.neuroimage.2017.08.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/21/2017] [Accepted: 08/09/2017] [Indexed: 01/22/2023] Open
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Hendriks AD, Luijten PR, Klomp DWJ, Petridou N. Potential acceleration performance of a 256-channel whole-brain receive array at 7 T. Magn Reson Med 2018; 81:1659-1670. [PMID: 30257049 PMCID: PMC6585755 DOI: 10.1002/mrm.27519] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/09/2018] [Accepted: 08/11/2018] [Indexed: 11/21/2022]
Abstract
Purpose Assess the potential gain in acceleration performance of a 256‐channel versus 32‐channel receive coil array at 7 T in combination with a 2D CAIPIRINHA sequence for 3D data sets. Methods A 256‐channel receive setup was simulated by placing 2 small 16‐channel high‐density receive arrays at 2 × 8 different locations on the head of healthy participants. Multiple consecutive measurements were performed and coil sensitivity maps were combined to form a complete 256‐channel data set. This setup was compared with a standard 32‐channel head coil, in terms of SNR, noise correlation, and acceleration performance (g‐factor). Results In the periphery of the brain, the receive SNR was on average a factor 1.5 higher (ranging up to a factor 2.7 higher) than the 32‐channel coil; in the center of the brain the SNR was comparable or lower, depending on the size of the region of interest, with a factor 1.0 on average (ranging from 0.7 up to a factor of 1.6). The average noise correlation between coil elements was 3% for the 256‐channel coil, and 5% for the 32‐channel coil. At acceptable g‐factors (< 2), the achievable acceleration factor using SENSE and 2D CAIPIRINHA was 24 and 28, respectively, versus 9 and 12 for the 32‐channel coil. Conclusion The receive performance of the simulated 256 channel array was better than the 32‐channel reference. Combined with 2D CAIPIRINHA, a peak acceleration factor of 28 was assessed, showing great potential for high‐density receive arrays.
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Affiliation(s)
- Arjan D Hendriks
- Department of Radiology, Imaging Division, University Medical Center Utrecht, Utrecht, Netherlands
| | - Peter R Luijten
- Department of Radiology, Imaging Division, University Medical Center Utrecht, Utrecht, Netherlands
| | - Dennis W J Klomp
- Department of Radiology, Imaging Division, University Medical Center Utrecht, Utrecht, Netherlands
| | - Natalia Petridou
- Department of Radiology, Imaging Division, University Medical Center Utrecht, Utrecht, Netherlands
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The State of the NIH BRAIN Initiative. J Neurosci 2018; 38:6427-6438. [PMID: 29921715 DOI: 10.1523/jneurosci.3174-17.2018] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022] Open
Abstract
The BRAIN Initiative arose from a grand challenge to "accelerate the development and application of new technologies that will enable researchers to produce dynamic pictures of the brain that show how individual brain cells and complex neural circuits interact at the speed of thought." The BRAIN Initiative is a public-private effort focused on the development and use of powerful tools for acquiring fundamental insights about how information processing occurs in the central nervous system (CNS). As the Initiative enters its fifth year, NIH has supported >500 principal investigators, who have answered the Initiative's challenge via hundreds of publications describing novel tools, methods, and discoveries that address the Initiative's seven scientific priorities. We describe scientific advances produced by individual laboratories, multi-investigator teams, and entire consortia that, over the coming decades, will produce more comprehensive and dynamic maps of the brain, deepen our understanding of how circuit activity can produce a rich tapestry of behaviors, and lay the foundation for understanding how its circuitry is disrupted in brain disorders. Much more work remains to bring this vision to fruition, and the National Institutes of Health continues to look to the diverse scientific community, from mathematics, to physics, chemistry, engineering, neuroethics, and neuroscience, to ensure that the greatest scientific benefit arises from this unique research Initiative.
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Yoshida Y, Nakao M, Katayama N. Resting-state functional connectivity analysis of the mouse brain using intrinsic optical signal imaging of cerebral blood volume dynamics. Physiol Meas 2018; 39:054003. [PMID: 29697052 DOI: 10.1088/1361-6579/aac033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Resting-state functional connectivity (rsFC) of the human brain is closely related with neurological and psychiatric disorders. Mice are widely used to investigate the physiological mechanisms of such disorders, because of the applicability of invasive experimental techniques. Thus, studies on rsFC of the mouse brain are essential to link physiological mechanisms with these disorders in humans. In this study, we investigated the applicability of intrinsic optical signal imaging of cerebral blood volume (IOSI-CBV) for rsFC analysis of the mouse brain. APPROACH Transcranial IOSI-CBV images were collected from the brains of un-anesthetized wild-type mice with a cooled-CCD camera. The time traces of all pixels were averaged to create a global signal (GS). Marginal and partial correlation analyses were performed to estimate the rsFC based on CBV signals both with and without GS removal. The consistency of the results were confirmed by comparing them with to the rsFCs data reported in the previous studies. MAIN RESULTS We confirmed that GS correlated with heart rate fluctuation in the FC frequency band. The marginal correlation coefficient of CBV with GS removal was consistent with measurements using conventional optical imaging methods relying on oxygenated hemoglobin concentration and cerebral blood flow. SIGNIFICANCE These results suggest the applicability and usefulness of the transcranial IOSI-CBV method to estimate rsFC of the mouse brain.
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Affiliation(s)
- Yuto Yoshida
- Research Fellow of Japan Society for the Promotion of Science (JSPS), 6-6-05, Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi prefecture, 980-8579, Japan. Biomodeling Laboratory, Graduate School of Information Sciences, Tohoku University, 6-6-05, Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi prefecture, 980-8579, Japan
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Foo TKF, Laskaris E, Vermilyea M, Xu M, Thompson P, Conte G, Van Epps C, Immer C, Lee SK, Tan ET, Graziani D, Mathieu JB, Hardy CJ, Schenck JF, Fiveland E, Stautner W, Ricci J, Piel J, Park K, Hua Y, Bai Y, Kagan A, Stanley D, Weavers PT, Gray E, Shu Y, Frick MA, Campeau NG, Trzasko J, Huston J, Bernstein MA. Lightweight, compact, and high-performance 3T MR system for imaging the brain and extremities. Magn Reson Med 2018. [PMID: 29536587 DOI: 10.1002/mrm.27175] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE To build and evaluate a small-footprint, lightweight, high-performance 3T MRI scanner for advanced brain imaging with image quality that is equal to or better than conventional whole-body clinical 3T MRI scanners, while achieving substantial reductions in installation costs. METHODS A conduction-cooled magnet was developed that uses less than 12 liters of liquid helium in a gas-charged sealed system, and standard NbTi wire, and weighs approximately 2000 kg. A 42-cm inner-diameter gradient coil with asymmetric transverse axes was developed to provide patient access for head and extremity exams, while minimizing magnet-gradient interactions that adversely affect image quality. The gradient coil was designed to achieve simultaneous operation of 80-mT/m peak gradient amplitude at a slew rate of 700 T/m/s on each gradient axis using readily available 1-MVA gradient drivers. RESULTS In a comparison of anatomical imaging in 16 patients using T2 -weighted 3D fluid-attenuated inversion recovery (FLAIR) between the compact 3T and whole-body 3T, image quality was assessed as equivalent to or better across several metrics. The ability to fully use a high slew rate of 700 T/m/s simultaneously with 80-mT/m maximum gradient amplitude resulted in improvements in image quality across EPI, DWI, and anatomical imaging of the brain. CONCLUSIONS The compact 3T MRI system has been in continuous operation at the Mayo Clinic since March 2016. To date, over 200 patient studies have been completed, including 96 comparison studies with a clinical 3T whole-body MRI. The increased gradient performance has reliably resulted in consistently improved image quality.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Seung-Kyun Lee
- GE Global Research, Niskayuna, New York.,Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Ek T Tan
- GE Global Research, Niskayuna, New York
| | | | | | | | | | | | | | | | | | | | - Yihe Hua
- GE Global Research, Niskayuna, New York
| | - Ye Bai
- GE Global Research, Niskayuna, New York
| | | | | | - Paul T Weavers
- Department of Radiology, Mayo Clinic, Rochester, Minnesota.,GE Healthcare, Waukesha, Wisconsin
| | - Erin Gray
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
| | - Yunhong Shu
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Joshua Trzasko
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
| | - John Huston
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
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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: 2.3] [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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