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Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
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Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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2
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Mächler P, Fomin-Thunemann N, Thunemann M, Sætra MJ, Desjardins M, Kılıç K, Amra LN, Martin EA, Chen IA, Şencan-Eğilmez I, Li B, Saisan P, Jiang JX, Cheng Q, Weldy KL, Boas DA, Buxton RB, Einevoll GT, Dale AM, Sakadžić S, Devor A. Baseline oxygen consumption decreases with cortical depth. PLoS Biol 2022; 20:e3001440. [PMID: 36301995 PMCID: PMC9642908 DOI: 10.1371/journal.pbio.3001440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/08/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022] Open
Abstract
The cerebral cortex is organized in cortical layers that differ in their cellular density, composition, and wiring. Cortical laminar architecture is also readily revealed by staining for cytochrome oxidase-the last enzyme in the respiratory electron transport chain located in the inner mitochondrial membrane. It has been hypothesized that a high-density band of cytochrome oxidase in cortical layer IV reflects higher oxygen consumption under baseline (unstimulated) conditions. Here, we tested the above hypothesis using direct measurements of the partial pressure of O2 (pO2) in cortical tissue by means of 2-photon phosphorescence lifetime microscopy (2PLM). We revisited our previously developed method for extraction of the cerebral metabolic rate of O2 (CMRO2) based on 2-photon pO2 measurements around diving arterioles and applied this method to estimate baseline CMRO2 in awake mice across cortical layers. To our surprise, our results revealed a decrease in baseline CMRO2 from layer I to layer IV. This decrease of CMRO2 with cortical depth was paralleled by an increase in tissue oxygenation. Higher baseline oxygenation and cytochrome density in layer IV may serve as an O2 reserve during surges of neuronal activity or certain metabolically active brain states rather than reflecting baseline energy needs. Our study provides to our knowledge the first quantification of microscopically resolved CMRO2 across cortical layers as a step towards better understanding of brain energy metabolism.
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Affiliation(s)
- Philipp Mächler
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Natalie Fomin-Thunemann
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Martin Thunemann
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Marte Julie Sætra
- Department of Numerical Analysis and Scientific Computing, Simula Research Laboratory, Oslo, Norway
| | - Michèle Desjardins
- Département de Physique, de Génie Physique et d’Optique and Axe Oncologie, Centre de Recherche du CHU de Québec–Université Laval, Université Laval, Québec, Canada
| | - Kıvılcım Kılıç
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Layth N. Amra
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Emily A. Martin
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Ichun Anderson Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Ikbal Şencan-Eğilmez
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Baoqiang Li
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Payam Saisan
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - John X. Jiang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Qun Cheng
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Kimberly L. Weldy
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - David A. Boas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Richard B. Buxton
- Department of Radiology, University of California San Diego, La Jolla, California, United States of America
| | - Gaute T. Einevoll
- Department of Physics, University of Oslo, Oslo, Norway
- Department of Physics, Norwegian University of Life Sciences, Ås, Norway
| | - Anders M. Dale
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
- Department of Radiology, University of California San Diego, La Jolla, California, United States of America
| | - Sava Sakadžić
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- * E-mail: (SS); (AD)
| | - Anna Devor
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- * E-mail: (SS); (AD)
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3
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Wang J, Nasr S, Roe AW, Polimeni JR. Critical factors in achieving fine-scale functional MRI: Removing sources of inadvertent spatial smoothing. Hum Brain Mapp 2022; 43:3311-3331. [PMID: 35417073 PMCID: PMC9248309 DOI: 10.1002/hbm.25867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 11/09/2022] Open
Abstract
Ultra‐high Field (≥7T) functional magnetic resonance imaging (UHF‐fMRI) provides opportunities to resolve fine‐scale features of functional architecture such as cerebral cortical columns and layers, in vivo. While the nominal resolution of modern fMRI acquisitions may appear to be sufficient to resolve these features, several common data preprocessing steps can introduce unwanted spatial blurring, especially those that require interpolation of the data. These resolution losses can impede the detection of the fine‐scale features of interest. To examine quantitatively and systematically the sources of spatial resolution losses occurring during preprocessing, we used synthetic fMRI data and real fMRI data from the human visual cortex—the spatially interdigitated human V2 “thin” and “thick” stripes. The pattern of these cortical columns lies along the cortical surface and thus can be best appreciated using surface‐based fMRI analysis. We used this as a testbed for evaluating strategies that can reduce spatial blurring of fMRI data. Our results show that resolution losses can be mitigated at multiple points in preprocessing pathway. We show that unwanted blur is introduced at each step of volume transformation and surface projection, and can be ameliorated by replacing multi‐step transformations with equivalent single‐step transformations. Surprisingly, the simple approaches of volume upsampling and of cortical mesh refinement also helped to reduce resolution losses caused by interpolation. Volume upsampling also serves to improve motion estimation accuracy, which helps to reduce blur. Moreover, we demonstrate that the level of spatial blurring is nonuniform over the brain—knowledge which is critical for interpreting data in high‐resolution fMRI studies. Importantly, our study provides recommendations for reducing unwanted blurring during preprocessing as well as methods that enable quantitative comparisons between preprocessing strategies. These findings highlight several underappreciated sources of a spatial blur. Individually, the factors that contribute to spatial blur may appear to be minor, but in combination, the cumulative effects can hinder the interpretation of fine‐scale fMRI and the detectability of these fine‐scale features of functional architecture.
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Affiliation(s)
- Jianbao Wang
- Department of Neurosurgery of the Second Affiliated Hospital, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, China.,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Shahin Nasr
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Anna Wang Roe
- Department of Neurosurgery of the Second Affiliated Hospital, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Charlestown, Massachusetts, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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4
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The Global Configuration of Visual Stimuli Alters Co-Fluctuations of Cross-Hemispheric Human Brain Activity. J Neurosci 2021; 41:9756-9766. [PMID: 34663628 DOI: 10.1523/jneurosci.3214-20.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 09/11/2021] [Accepted: 10/07/2021] [Indexed: 11/21/2022] Open
Abstract
We tested how a stimulus gestalt, defined by the neuronal interaction between local and global features of a stimulus, is represented within human primary visual cortex (V1). We used high-resolution fMRI, which serves as a surrogate of neuronal activation, to measure co-fluctuations within subregions of V1 as (male and female) subjects were presented with peripheral stimuli, each with different global configurations. We found stronger cross-hemisphere correlations when fine-scale V1 cortical subregions represented parts of the same object compared with different objects. This result was consistent with the vertical bias in global processing and, critically, was independent of the task and local discontinuities within objects. Thus, despite the relatively small receptive fields of neurons within V1, global stimulus configuration affects neuronal processing via correlated fluctuations between regions that represent different sectors of the visual field.SIGNIFICANCE STATEMENT We provide the first evidence for the impact of global stimulus configuration on cross-hemispheric fMRI fluctuations, measured in human primary visual cortex. Our results are consistent with changes in the level of γ-band synchrony, which has been shown to be affected by global stimulus configuration, being reflected in the level fMRI co-fluctuations. These data help narrow the gap between knowledge of global stimulus configuration encoding at the single-neuron level versus at the behavioral level.
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5
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Imaging faster neural dynamics with fast fMRI: A need for updated models of the hemodynamic response. Prog Neurobiol 2021; 207:102174. [PMID: 34525404 DOI: 10.1016/j.pneurobio.2021.102174] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 07/30/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022]
Abstract
Fast fMRI enables the detection of neural dynamics over timescales of hundreds of milliseconds, suggesting it may provide a new avenue for studying subsecond neural processes in the human brain. The magnitudes of these fast fMRI dynamics are far greater than predicted by canonical models of the hemodynamic response. Several studies have established nonlinear properties of the hemodynamic response that have significant implications for fast fMRI. We first review nonlinear properties of the hemodynamic response function that may underlie fast fMRI signals. We then illustrate the breakdown of canonical hemodynamic response models in the context of fast neural dynamics. We will then argue that the canonical hemodynamic response function is not likely to reflect the BOLD response to neuronal activity driven by sparse or naturalistic stimuli or perhaps to spontaneous neuronal fluctuations in the resting state. These properties suggest that fast fMRI is capable of tracking surprisingly fast neuronal dynamics, and we discuss the neuroscientific questions that could be addressed using this approach.
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6
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Vachha B, Huang SY. MRI with ultrahigh field strength and high-performance gradients: challenges and opportunities for clinical neuroimaging at 7 T and beyond. Eur Radiol Exp 2021; 5:35. [PMID: 34435246 PMCID: PMC8387544 DOI: 10.1186/s41747-021-00216-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Research in ultrahigh magnetic field strength combined with ultrahigh and ultrafast gradient technology has provided enormous gains in sensitivity, resolution, and contrast for neuroimaging. This article provides an overview of the technical advantages and challenges of performing clinical neuroimaging studies at ultrahigh magnetic field strength combined with ultrahigh and ultrafast gradient technology. Emerging clinical applications of 7-T MRI and state-of-the-art gradient systems equipped with up to 300 mT/m gradient strength are reviewed, and the impact and benefits of such advances to anatomical, structural and functional MRI are discussed in a variety of neurological conditions. Finally, an outlook and future directions for ultrahigh field MRI combined with ultrahigh and ultrafast gradient technology in neuroimaging are examined.
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Affiliation(s)
- Behroze Vachha
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Susie Y Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, 149 13th Street, Room 2301, Charlestown, MA, 02129, USA.
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7
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Yang J, Huber L, Yu Y, Bandettini PA. Linking cortical circuit models to human cognition with laminar fMRI. Neurosci Biobehav Rev 2021; 128:467-478. [PMID: 34245758 DOI: 10.1016/j.neubiorev.2021.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Laboratory animal research has provided significant knowledge into the function of cortical circuits at the laminar level, which has yet to be fully leveraged towards insights about human brain function on a similar spatiotemporal scale. The use of functional magnetic resonance imaging (fMRI) in conjunction with neural models provides new opportunities to gain important insights from current knowledge. During the last five years, human studies have demonstrated the value of high-resolution fMRI to study laminar-specific activity in the human brain. This is mostly performed at ultra-high-field strengths (≥ 7 T) and is known as laminar fMRI. Advancements in laminar fMRI are beginning to open new possibilities for studying questions in basic cognitive neuroscience. In this paper, we first review recent methodological advances in laminar fMRI and describe recent human laminar fMRI studies. Then, we discuss how the use of laminar fMRI can help bridge the gap between cortical circuit models and human cognition.
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Affiliation(s)
- Jiajia Yang
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan; Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA.
| | - Laurentius Huber
- MR-Methods Group, Faculty of Psychology and Neuroscience, University of Maastricht, Maastricht, the Netherlands
| | - Yinghua Yu
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan; Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA
| | - Peter A Bandettini
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA; Functional MRI Core Facility, National Institute of Mental Health, Bethesda, MD, USA
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8
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Ding W, Ding L, Zhu J, Li L, Ding F. Application of Magnetic Resonance-Ultra Time Echo (MR-UTE) Imaging in the Analysis of the Degree of Degeneration of the Intervertebral Disc Cartilage Endplate. JOURNAL OF MEDICAL IMAGING AND HEALTH INFORMATICS 2021. [DOI: 10.1166/jmihi.2021.3711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Magnetic resonance imaging (MRI) is the most widely used imaging method in clinical lumbar spine examination. Because of its advantages of non-radiation and good tissue contrast, magnetic resonance imaging provides rich and effective diagnostic information for clinic. The most commonly
used sequence is type 2 (T2) sequence, which has a longer time (usually longer than 2000 ms). It shows well in long T2 tissues such as nucleus pulposus, cerebrospinal fluid and adipose tissue, showing moderator high signal in images, while for short T2
tissues such as cartilage endplate and anterior and posterior longitudinal zone, it is often no signal and low signal because of its short attenuation time, thus forming obvious tissue contrast. But at the same time, because the time is too long, for short T2 tissue, the signal
has been attenuated to zero before sequence acquisition, so the complete structure can not be displayed directly. In this paper, the normal human lumbar intervertebral disc was studied by conventional magnetic resonance type 1 (T1), T2 and double-echo-UTE
imaging techniques. Each part of lumbar intervertebral disc and the semi-quantitative analysis of anatomical structure in images were compared, and the advantages and characteristics of each sequence for each anatomical structure of lumbar intervertebral disc and the advantage of MR-UTE in
intervertebral disc display were discussed. It has been found that UTE, as a new sequence which can effectively image short T2 tissue, is gradually applied from experiment to clinic in bone and joint system because of its shorter time. In the gross specimens of lumbar intervertebral
disc, sequence can directly display the cartilage endplate and the short T2 tissue of the anterior and posterior longitudinal ligament.
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Affiliation(s)
- Weiwei Ding
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan Ningxia, 750004, China
| | - Lei Ding
- Department of Orthopedics, The Yinchuan No. 1 People’s Hospital, Yinchuan Ningxia, 750001, China
| | - Jinwen Zhu
- The Spine Hospital of Xi’an Honghui Hospital, Xi’an Shaanxi, 710054, China
| | - Li Li
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan Ningxia, 750004, China
| | - Feng Ding
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan Ningxia, 750004, China
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9
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Viessmann O, Polimeni JR. High-resolution fMRI at 7 Tesla: challenges, promises and recent developments for individual-focused fMRI studies. Curr Opin Behav Sci 2021; 40:96-104. [PMID: 33816717 DOI: 10.1016/j.cobeha.2021.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Limited detection power has been a bottleneck for subject-specific functional MRI (fMRI) studies, however the higher signal-to-noise ratio afforded by ultra-high magnetic fields (≥ 7 Tesla) provides levels of sensitivity and resolution needed to study individual subjects. What may be surprising is that higher imaging resolution may provide both higher specificity and sensitivity due to reductions in partial volume effects and reduced physiological noise. However, challenges remain to ensure high data quality and to reduce variability in ultra-high field fMRI. We discuss session-specific biases including those caused by factors related to instrumentation, anatomy, and physiology-which can translate into variability across sessions-and how to minimize these to help ultra-high field fMRI reach its full potential for individual-focused studies.
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Affiliation(s)
- Olivia Viessmann
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Radiology, Harvard Medical School, Boston, MA, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
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10
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Tian Q, Bilgic B, Fan Q, Ngamsombat C, Zaretskaya N, Fultz NE, Ohringer NA, Chaudhari AS, Hu Y, Witzel T, Setsompop K, Polimeni JR, Huang SY. Improving in vivo human cerebral cortical surface reconstruction using data-driven super-resolution. Cereb Cortex 2021; 31:463-482. [PMID: 32887984 PMCID: PMC7727379 DOI: 10.1093/cercor/bhaa237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 11/14/2022] Open
Abstract
Accurate and automated reconstruction of the in vivo human cerebral cortical surface from anatomical magnetic resonance (MR) images facilitates the quantitative analysis of cortical structure. Anatomical MR images with sub-millimeter isotropic spatial resolution improve the accuracy of cortical surface and thickness estimation compared to the standard 1-millimeter isotropic resolution. Nonetheless, sub-millimeter resolution acquisitions require averaging multiple repetitions to achieve sufficient signal-to-noise ratio and are therefore long and potentially vulnerable to subject motion. We address this challenge by synthesizing sub-millimeter resolution images from standard 1-millimeter isotropic resolution images using a data-driven supervised machine learning-based super-resolution approach achieved via a deep convolutional neural network. We systematically characterize our approach using a large-scale simulated dataset and demonstrate its efficacy in empirical data. The super-resolution data provide improved cortical surfaces similar to those obtained from native sub-millimeter resolution data. The whole-brain mean absolute discrepancy in cortical surface positioning and thickness estimation is below 100 μm at the single-subject level and below 50 μm at the group level for the simulated data, and below 200 μm at the single-subject level and below 100 μm at the group level for the empirical data, making the accuracy of cortical surfaces derived from super-resolution sufficient for most applications.
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Affiliation(s)
- Qiyuan Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Qiuyun Fan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Chanon Ngamsombat
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
| | - Natalia Zaretskaya
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Experimental Psychology and Cognitive Neuroscience, Institute of Psychology, University of Graz, Graz, Austria
- BioTechMed-Graz, Austria
| | - Nina E Fultz
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
| | - Ned A Ohringer
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
| | - Akshay S Chaudhari
- Radiological Sciences Laboratory, Department of Radiology, Stanford University, Stanford, CA, United States
| | - Yuxin Hu
- Radiological Sciences Laboratory, Department of Radiology, Stanford University, Stanford, CA, United States
| | - Thomas Witzel
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Susie Y Huang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, United States
- Harvard Medical School, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
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11
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Berman AJL, Grissom WA, Witzel T, Nasr S, Park DJ, Setsompop K, Polimeni JR. Ultra-high spatial resolution BOLD fMRI in humans using combined segmented-accelerated VFA-FLEET with a recursive RF pulse design. Magn Reson Med 2020; 85:120-139. [PMID: 32705723 DOI: 10.1002/mrm.28415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 11/08/2022]
Abstract
PURPOSE To alleviate the spatial encoding limitations of single-shot echo-planar imaging (EPI) by developing multi-shot segmented EPI for ultra-high-resolution functional MRI (fMRI) with reduced ghosting artifacts from subject motion and respiration. THEORY AND METHODS Segmented EPI can reduce readout duration and reduce acceleration factors, however, the time elapsed between segment acquisitions (on the order of seconds) can result in intermittent ghosting, limiting its use for fMRI. Here, "FLEET" segment ordering, where segments are looped over before slices, was combined with a variable flip angle progression (VFA-FLEET) to improve inter-segment fidelity and maximize signal for fMRI. Scaling a sinc pulse's flip angle for each segment (VFA-FLEET-Sinc) produced inconsistent slice profiles and ghosting, therefore, a recursive Shinnar-Le Roux (SLR) radiofrequency (RF) pulse design was developed (VFA-FLEET-SLR) to generate unique pulses for every segment that together produce consistent slice profiles and signals. RESULTS The temporal stability of VFA-FLEET-SLR was compared against conventional-segmented EPI and VFA-FLEET-Sinc at 3T and 7T. VFA-FLEET-SLR showed reductions in both intermittent and stable ghosting compared to conventional-segmented and VFA-FLEET-Sinc, resulting in improved image quality with a minor trade-off in temporal SNR. Combining VFA-FLEET-SLR with acceleration, we achieved a 0.6-mm isotropic acquisition at 7T, without zoomed imaging or partial Fourier, demonstrating reliable detection of blood oxygenation level-dependent (BOLD) responses to a visual stimulus. To counteract the increased repetition time from segmentation, simultaneous multi-slice VFA-FLEET-SLR was demonstrated using RF-encoded controlled aliasing. CONCLUSIONS VFA-FLEET with a recursive RF pulse design supports acquisitions with low levels of artifact and spatial blur, enabling fMRI at previously inaccessible spatial resolutions with a "full-brain" field of view.
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Affiliation(s)
- Avery J L Berman
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - William A Grissom
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Thomas Witzel
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shahin Nasr
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel J Park
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Radiologic evidence that hypothalamic gliosis is improved after bariatric surgery in obese women with type 2 diabetes. Int J Obes (Lond) 2019; 44:178-185. [PMID: 31201362 PMCID: PMC7366782 DOI: 10.1038/s41366-019-0399-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/10/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND/OBJECTIVES Hypothalamic neurons play a major role in the control of body mass. Obese subjects present radiologic signs of gliosis in the hypothalamus, which may reflect the damage or loss of neurons involved in whole-body energy homeostasis. It is currently unknown if hypothalamic gliosis (1) differs between obese nondiabetic (ND) and obese diabetic subjects (T2D) or (2) is modified by extensive body mass reduction via Roux-n-Y gastric bypass (RYGB). SUBJECTS/METHODS Fifty-five subjects (all female) including lean controls (CT; n = 13), ND (n = 28), and T2D (n = 14) completed at least one study visit. Subjects underwent anthropometrics and a multi-echo MRI sequence to measure mean bilateral T2 relaxation time in the mediobasal hypothalamus (MBH) and two reference regions (amygdala and putamen). The obese groups underwent RYGB and were re-evaluated 9 months later. Analyses were by linear mixed models. RESULTS Analyses of T2 relaxation time at baseline showed a group by region interaction only in the MBH (P < 0.0001). T2D had longer T2 relaxation times compared to either CT or ND groups. To examine the effects of RYGB on hypothalamic gliosis a three-way (group by region by time) mixed effects model adjusted for age was executed. Group by region (P < 0.0001) and region by time (P = 0.0005) interactions were significant. There was a reduction in MBH relaxation time by RYGB, and, although the T2D group still had higher T2 relaxation time overall compared to the ND group, the T2D group had significantly lower T2 relaxation time after surgery and the ND group showed a trend. The degree of reduction in MBH T2 relaxation time by RYGB was unrelated to clinical outcomes. CONCLUSION T2 relaxation times, a marker of hypothalamic gliosis, are higher in obese women with T2D and are reduced by RYGB-induced weight loss.
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Viessmann O, Scheffler K, Bianciardi M, Wald LL, Polimeni JR. Dependence of resting-state fMRI fluctuation amplitudes on cerebral cortical orientation relative to the direction of B0 and anatomical axes. Neuroimage 2019; 196:337-350. [PMID: 31002965 DOI: 10.1016/j.neuroimage.2019.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/30/2019] [Accepted: 04/11/2019] [Indexed: 01/21/2023] Open
Abstract
Functional magnetic resonance imaging (fMRI) is now capable of sub-millimetre scale measurements over the entire human brain, however with such high resolutions each voxel is influenced by the local fine-scale details of the cerebral cortical vascular anatomy. The cortical vasculature is structured with the pial vessels lying tangentially along the grey matter surface, intracortical diving arterioles and ascending venules running perpendicularly to the surface, and a randomly oriented capillary network within the parenchyma. It is well-known that the amplitude of the blood-oxygenation level dependent (BOLD) signal emanating from a vessel depends on its orientation relative to the B0-field. Thus the vascular geometric hierarchy will impart an orientation dependence to the BOLD signal amplitudes and amplitude differences due to orientation differences constitute a bias for interpreting neuronal activity. Here, we demonstrate a clear effect of cortical orientation to B0 in the resting-state BOLD-fMRI amplitude (quantified as the coefficient of temporal signal variation) for 1.1 mm isotropic data at 7T and 2 mm isotropic at 3T. The maximum bias, i.e. the fluctuation amplitude difference between regions where cortex is perpendicular to vs. parallel to B0, is about +70% at the pial surface at 7T and +11% at 3T. The B0 orientation bias declines with cortical depth, becomes progressively smaller closer to the white matter surface, but then increases again to a local maximum within the white matter just beneath the cortical grey matter, suggesting a distinct tangential network of white matter vessels that also generate a BOLD orientation effect. We further found significant (negative) biases with the cortex orientation to the anterior-posterior anatomical axis of the head: a maximum negative bias of about -30% at the pial surface at 7T and about -13% at 3T. The amount of signal variance explained by the low frequency drift, motion and the respiratory cycle also showed a cortical orientation dependence; only the cardiac cycle induced signal variance was independent of cortical orientation, suggesting that the cardiac induced component of the image time-series fluctuations is not related to a significant change in susceptibility. Although these orientation effects represent a signal bias, and are likely to be a nuisance in high-resolution analyses, they may help characterize the vascular influences on candidate fMRI acquisitions and, thereby, may be exploited to improve the neuronal specificity of fMRI.
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Affiliation(s)
- Olivia Viessmann
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 13th St., Charlestown, Boston, MA 02129, USA.
| | - Klaus Scheffler
- Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 11, 72076 Tübingen, Germany.
| | - Marta Bianciardi
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 13th St., Charlestown, Boston, MA 02129, USA.
| | - Lawrence L Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 13th St., Charlestown, Boston, MA 02129, USA; Harvard-Massachusetts Institute of Technology, Division of Health Sciences and Technology, Cambridge, MA, USA.
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149 13th St., Charlestown, Boston, MA 02129, USA; Harvard-Massachusetts Institute of Technology, Division of Health Sciences and Technology, Cambridge, MA, USA.
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