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Renton AI, Dao TT, Johnstone T, Civier O, Sullivan RP, White DJ, Lyons P, Slade BM, Abbott DF, Amos TJ, Bollmann S, Botting A, Campbell MEJ, Chang J, Close TG, Dörig M, Eckstein K, Egan GF, Evas S, Flandin G, Garner KG, Garrido MI, Ghosh SS, Grignard M, Halchenko YO, Hannan AJ, Heinsfeld AS, Huber L, Hughes ME, Kaczmarzyk JR, Kasper L, Kuhlmann L, Lou K, Mantilla-Ramos YJ, Mattingley JB, Meier ML, Morris J, Narayanan A, Pestilli F, Puce A, Ribeiro FL, Rogasch NC, Rorden C, Schira MM, Shaw TB, Sowman PF, Spitz G, Stewart AW, Ye X, Zhu JD, Narayanan A, Bollmann S. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nat Methods 2024; 21:804-808. [PMID: 38191935 DOI: 10.1038/s41592-023-02145-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.
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Affiliation(s)
- Angela I Renton
- The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia.
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.
| | - Thuy T Dao
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
| | - Tom Johnstone
- Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Oren Civier
- Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Ryan P Sullivan
- The University of Sydney, School of Biomedical Engineering, Sydney, New South Wales, Australia
| | - David J White
- Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Paris Lyons
- Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Benjamin M Slade
- Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - David F Abbott
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Toluwani J Amos
- School of Life Science and Technology, University of Electronic Science and Technology, Chengdu, China
| | - Saskia Bollmann
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
| | - Andy Botting
- Australian Research Data Commons (ARDC), Sydney, New South Wales, Australia
| | - Megan E J Campbell
- School of Psychological Sciences, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute Imaging Centre, Newcastle, New South Wales, Australia
| | - Jeryn Chang
- The University of Queensland, School of Biomedical Sciences, St Lucia, Brisbane, Queensland, Australia
| | - Thomas G Close
- The University of Sydney, School of Biomedical Engineering, Sydney, New South Wales, Australia
| | - Monika Dörig
- Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Korbinian Eckstein
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
| | - Gary F Egan
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
- Monash Biomedical Imaging, Monash University, Melbourne, Victoria, Australia
| | - Stefanie Evas
- School of Psychology, University of Adelaide, Adelaide, South Australia, Australia
- Human Health, Health & Biosecurity, CSIRO, Adelaide, South Australia, Australia
| | - Guillaume Flandin
- Wellcome Centre for Human Neuroimaging, University College London, London, UK
| | - Kelly G Garner
- School of Psychology, University of New South Wales, Sydney, New South Wales, Australia
- The University of Queensland, School of Psychology, St Lucia, Brisbane, Queensland, Australia
| | - Marta I Garrido
- Melbourne School of Psychological Sciences, he University of Melbourne, Melbourne, Victoria, Australia
- Graeme Clark Institute for Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia
| | - Satrajit S Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Martin Grignard
- GIGA CRC In-Vivo Imaging, University of Liège, Liège, Belgium
| | - Yaroslav O Halchenko
- Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anibal S Heinsfeld
- Department of Psychology, Center for Perceptual Systems, Institute for Neuroscience, Center For Learning and Memory, The University of Texas at Austin, Austin, TX, USA
| | - Laurentius Huber
- National Institute of Mental Health (NIMH), National Institutes Health, Bethesda, MD, USA
| | - Matthew E Hughes
- Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Jakub R Kaczmarzyk
- Department of Biomedical Informatics, Stony Brook University, New York, NY, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, New York, NY, USA
| | - Lars Kasper
- BRAIN-TO Lab, Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Levin Kuhlmann
- Department of Data Science and AI, Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Kexin Lou
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yorguin-Jose Mantilla-Ramos
- Grupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Jason B Mattingley
- The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia
- The University of Queensland, School of Psychology, St Lucia, Brisbane, Queensland, Australia
| | - Michael L Meier
- Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Jo Morris
- Australian Research Data Commons (ARDC), Sydney, New South Wales, Australia
| | - Akshaiy Narayanan
- School of Computer Science, The University of Auckland, Auckland, New Zealand
| | - Franco Pestilli
- Department of Psychology, Center for Perceptual Systems, Institute for Neuroscience, Center For Learning and Memory, The University of Texas at Austin, Austin, TX, USA
| | - Aina Puce
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Fernanda L Ribeiro
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
| | - Nigel C Rogasch
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Chris Rorden
- McCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, Columbia, SC, USA
| | - Mark M Schira
- School of Psychology, University of Wollongong, Wollongong, New South Wales, Australia
| | - Thomas B Shaw
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
- The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Paul F Sowman
- Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia
| | - Gershon Spitz
- Department of Neuroscience, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
- Monash-Epworth Rehabilitation Research Centre, Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Ashley W Stewart
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
- ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia
| | - Xincheng Ye
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia
| | - Judy D Zhu
- Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia
| | - Aswin Narayanan
- The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia
| | - Steffen Bollmann
- The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.
- The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia.
- ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia.
- Queensland Digital Health Centre, The University of Queensland, Brisbane, Queensland, Australia.
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Fan H, Mutsaerts HJ, Anazodo U, Arteaga D, Baas KP, Buchanan C, Camargo A, Keil VC, Lin Z, Lindner T, Hirschler L, Hu J, Padrela BE, Taghvaei M, Thomas DL, Dolui S, Petr J. ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory. Magn Reson Med 2024; 91:1787-1802. [PMID: 37811778 PMCID: PMC10950546 DOI: 10.1002/mrm.29869] [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: 03/03/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE To create an inventory of image processing pipelines of arterial spin labeling (ASL) and list their main features, and to evaluate the capability, flexibility, and ease of use of publicly available pipelines to guide novice ASL users in selecting their optimal pipeline. METHODS Developers self-assessed their pipelines using a questionnaire developed by the Task Force 1.1 of the ISMRM Open Science Initiative for Perfusion Imaging. Additionally, each publicly available pipeline was evaluated by two independent testers with basic ASL experience using a scoring system created for this purpose. RESULTS The developers of 21 pipelines filled the questionnaire. Most pipelines are free for noncommercial use (n = 18) and work with the standard NIfTI (Neuroimaging Informatics Technology Initiative) data format (n = 15). All pipelines can process standard 3D single postlabeling delay pseudo-continuous ASL images and primarily differ in their support of advanced sequences and features. The publicly available pipelines (n = 9) were included in the independent testing, all of them being free for noncommercial use. The pipelines, in general, provided a trade-off between ease of use and flexibility for configuring advanced processing options. CONCLUSION Although most ASL pipelines can process the common ASL data types, only some (namely, ASLPrep, ASLtbx, BASIL/Quantiphyse, ExploreASL, and MRICloud) are well-documented, publicly available, support multiple ASL types, have a user-friendly interface, and can provide a useful starting point for ASL processing. The choice of an optimal pipeline should be driven by specific data to be processed and user experience, and can be guided by the information provided in this ASL inventory.
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Affiliation(s)
- Hongli Fan
- The Johns Hopkins School of Medicine, Department of Biomedical Engineering, Baltimore, Maryland, USA
- MR Research and Development, Siemens Medical Solutions USA, Inc., Dallas, Texas, USA
| | - Henk J.M.M. Mutsaerts
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Udunna Anazodo
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Daniel Arteaga
- Ascension Saint Thomas Hospital, Nashville, Tennessee, USA
| | - Koen P.A. Baas
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
- Amsterdam UMC, Location AMC, Department of Radiology and Nuclear Medicine, Amsterdam, The Netherlands
| | - Charlotte Buchanan
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, United Kingdom
| | - Aldo Camargo
- School of Medicine, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland of Baltimore
| | - Vera C. Keil
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Zixuan Lin
- The Johns Hopkins School of Medicine, Department of Biomedical Engineering, Baltimore, Maryland, USA
| | - Thomas Lindner
- Department of Diagnostic and Interventional Neuroradiology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Lydiane Hirschler
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Jian Hu
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, United Kingdom
- Mental Health & Clinical Neurosciences, School of Medicine, University of Nottingham, United Kingdom
| | - Beatriz E. Padrela
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Mohammad Taghvaei
- Department of Radiology, University of Pennsylvania, Philadelphia, USA
| | - David L. Thomas
- Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Sudipto Dolui
- Department of Radiology, University of Pennsylvania, Philadelphia, USA
| | - Jan Petr
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
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3
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Dickie EW, Ameis SH, Boileau I, Diaconescu AO, Felsky D, Goldstein BI, Gonçalves V, Griffiths JD, Haltigan JD, Husain MO, Rubin-Kahana DS, Iftikhar M, Jani M, Lai MC, Lin HY, MacIntosh BJ, Wheeler AL, Vasdev N, Vieira E, Ahmadzadeh G, Heyland L, Mohan A, Ogunsanya F, Oliver LD, Zhu C, Wong JKY, Charlton C, Truong J, Yu L, Kelly R, Cleverley K, Courtney DB, Foussias G, Hawke LD, Hill S, Kozloff N, Polillo A, Rotenberg M, Quilty LC, Tempelaar W, Wang W, Nikolova YS, Voineskos AN. Neuroimaging and Biosample Collection in the Toronto Adolescent and Youth Cohort Study: Rationale, Methods, and Early Data. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2024; 9:275-284. [PMID: 37979944 DOI: 10.1016/j.bpsc.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND The Toronto Adolescent and Youth (TAY) Cohort Study will characterize the neurobiological trajectories of psychosis spectrum symptoms, functioning, and suicidality (i.e., suicidal thoughts and behaviors) in youth seeking mental health care. Here, we present the neuroimaging and biosample component of the protocol. We also present feasibility and quality control metrics for the baseline sample collected thus far. METHODS The current study includes youths (ages 11-24 years) who were referred to child and youth mental health services within a large tertiary care center in Toronto, Ontario, Canada, with target recruitment of 1500 participants. Participants were offered the opportunity to provide any or all of the following: 1) 1-hour magnetic resonance imaging (MRI) scan (electroencephalography if ineligible for or declined MRI), 2) blood sample for genomic and proteomic data (or saliva if blood collection was declined or not feasible) and urine sample, and 3) heart rate recording to assess respiratory sinus arrhythmia. RESULTS Of the first 417 participants who consented to participate between May 4, 2021, and February 2, 2023, 412 agreed to participate in the imaging and biosample protocol. Of these, 334 completed imaging, 341 provided a biosample, 338 completed respiratory sinus arrhythmia, and 316 completed all 3. Following quality control, data usability was high (MRI: T1-weighted 99%, diffusion-weighted imaging 99%, arterial spin labeling 90%, resting-state functional MRI 95%, task functional MRI 90%; electroencephalography: 83%; respiratory sinus arrhythmia: 99%). CONCLUSIONS The high consent rates, good completion rates, and high data usability reported here demonstrate the feasibility of collecting and using brain imaging and biosamples in a large clinical cohort of youths seeking mental health care.
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Affiliation(s)
- Erin W Dickie
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie H Ameis
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Isabelle Boileau
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andreea O Diaconescu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Felsky
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin I Goldstein
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Gonçalves
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John D Griffiths
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John D Haltigan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad O Husain
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dafna S Rubin-Kahana
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Myera Iftikhar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Melanie Jani
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; National Taiwan University Hospital and College of Medicine, Taiwan
| | - Hsiang-Yuan Lin
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Bradley J MacIntosh
- Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Oslo University Hospital, Oslo, Norway
| | - Anne L Wheeler
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Hospital for Sick Children, Neurosciences and Mental Health, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Neil Vasdev
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erica Vieira
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ghazaleh Ahmadzadeh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Lindsay Heyland
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Acadia University, Wolfville, Nova Scotia, Canada
| | - Akshay Mohan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Feyi Ogunsanya
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychology, Western University, London, Ontario, Canada
| | - Lindsay D Oliver
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Cherrie Zhu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Sinai Health, Toronto, Ontario, Canada
| | - Jimmy K Y Wong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Colleen Charlton
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Jennifer Truong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Lujia Yu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Rachel Kelly
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Kristin Cleverley
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Darren B Courtney
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - George Foussias
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lisa D Hawke
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sean Hill
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Nicole Kozloff
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alexia Polillo
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Martin Rotenberg
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lena C Quilty
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wanda Tempelaar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wei Wang
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Yuliya S Nikolova
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aristotle N Voineskos
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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4
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Sollmann N, Hoffmann G, Schramm S, Reichert M, Hernandez Petzsche M, Strobel J, Nigris L, Kloth C, Rosskopf J, Börner C, Bonfert M, Berndt M, Grön G, Müller HP, Kassubek J, Kreiser K, Koerte IK, Liebl H, Beer A, Zimmer C, Beer M, Kaczmarz S. Arterial Spin Labeling (ASL) in Neuroradiological Diagnostics - Methodological Overview and Use Cases. ROFO-FORTSCHR RONTG 2024; 196:36-51. [PMID: 37467779 DOI: 10.1055/a-2119-5574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
BACKGROUND Arterial spin labeling (ASL) is a magnetic resonance imaging (MRI)-based technique using labeled blood-water of the brain-feeding arteries as an endogenous tracer to derive information about brain perfusion. It enables the assessment of cerebral blood flow (CBF). METHOD This review aims to provide a methodological and technical overview of ASL techniques, and to give examples of clinical use cases for various diseases affecting the central nervous system (CNS). There is a special focus on recent developments including super-selective ASL (ssASL) and time-resolved ASL-based magnetic resonance angiography (MRA) and on diseases commonly not leading to characteristic alterations on conventional structural MRI (e. g., concussion or migraine). RESULTS ASL-derived CBF may represent a clinically relevant parameter in various pathologies such as cerebrovascular diseases, neoplasms, or neurodegenerative diseases. Furthermore, ASL has also been used to investigate CBF in mild traumatic brain injury or migraine, potentially leading to the establishment of imaging-based biomarkers. Recent advances made possible the acquisition of ssASL by selective labeling of single brain-feeding arteries, enabling spatial perfusion territory mapping dependent on blood flow of a specific preselected artery. Furthermore, ASL-based MRA has been introduced, providing time-resolved delineation of single intracranial vessels. CONCLUSION Perfusion imaging by ASL has shown promise in various diseases of the CNS. Given that ASL does not require intravenous administration of a gadolinium-based contrast agent, it may be of particular interest for investigations in pediatric cohorts, patients with impaired kidney function, patients with relevant allergies, or patients that undergo serial MRI for clinical indications such as disease monitoring. KEY POINTS · ASL is an MRI technique that uses labeled blood-water as an endogenous tracer for brain perfusion imaging.. · It allows the assessment of CBF without the need for administration of a gadolinium-based contrast agent.. · CBF quantification by ASL has been used in several pathologies including brain tumors or neurodegenerative diseases.. · Vessel-selective ASL methods can provide brain perfusion territory mapping in cerebrovascular diseases.. · ASL may be of particular interest in patient cohorts with caveats concerning gadolinium administration..
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Affiliation(s)
- Nico Sollmann
- Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- TUM-Neuroimaging Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- cBrain, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gabriel Hoffmann
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- TUM-Neuroimaging Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Severin Schramm
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Miriam Reichert
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Moritz Hernandez Petzsche
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Joachim Strobel
- Department of Nuclear Medicine, University Hospital Ulm, Ulm, Germany
| | - Lorenzo Nigris
- cBrain, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christopher Kloth
- Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
| | - Johannes Rosskopf
- Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
- Section of Neuroradiology, Bezirkskrankenhaus Günzburg, Günzburg, Germany
| | - Corinna Börner
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- LMU Hospital, Department of Pediatrics - Dr. von Hauner Children's Hospital, Division of Pediatric Neurology and Developmental Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- LMU Center for Children with Medical Complexity - iSPZ Hauner, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michaela Bonfert
- LMU Hospital, Department of Pediatrics - Dr. von Hauner Children's Hospital, Division of Pediatric Neurology and Developmental Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- LMU Center for Children with Medical Complexity - iSPZ Hauner, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maria Berndt
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Georg Grön
- Department of Psychiatry and Psychotherapy III, University Hospital Ulm, Ulm, Germany
| | | | - Jan Kassubek
- Department of Neurology, University Hospital Ulm, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE), Ulm University, Ulm, Germany
| | - Kornelia Kreiser
- Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
- Department of Radiology and Neuroradiology, Universitäts- und Rehabilitationskliniken Ulm, Ulm, Germany
| | - Inga K Koerte
- cBrain, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-Universität München, Munich, Germany
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, United States
- Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, United States
| | - Hans Liebl
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Radiology, Berufsgenossenschaftliche Unfallklinik Murnau, Murnau, Germany
| | - Ambros Beer
- Department of Nuclear Medicine, University Hospital Ulm, Ulm, Germany
- MoMan - Center for Translational Imaging, University Hospital Ulm, Ulm, Germany
- i2SouI - Innovative Imaging in Surgical Oncology, University Hospital Ulm, Ulm, Germany
| | - Claus Zimmer
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- TUM-Neuroimaging Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Meinrad Beer
- Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
- MoMan - Center for Translational Imaging, University Hospital Ulm, Ulm, Germany
- i2SouI - Innovative Imaging in Surgical Oncology, University Hospital Ulm, Ulm, Germany
| | - Stephan Kaczmarz
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- TUM-Neuroimaging Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Market DACH, Philips GmbH, Hamburg, Germany
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5
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Bazinet V, Hansen JY, Misic B. Towards a biologically annotated brain connectome. Nat Rev Neurosci 2023; 24:747-760. [PMID: 37848663 DOI: 10.1038/s41583-023-00752-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
The brain is a network of interleaved neural circuits. In modern connectomics, brain connectivity is typically encoded as a network of nodes and edges, abstracting away the rich biological detail of local neuronal populations. Yet biological annotations for network nodes - such as gene expression, cytoarchitecture, neurotransmitter receptors or intrinsic dynamics - can be readily measured and overlaid on network models. Here we review how connectomes can be represented and analysed as annotated networks. Annotated connectomes allow us to reconceptualize architectural features of networks and to relate the connection patterns of brain regions to their underlying biology. Emerging work demonstrates that annotated connectomes help to make more veridical models of brain network formation, neural dynamics and disease propagation. Finally, annotations can be used to infer entirely new inter-regional relationships and to construct new types of network that complement existing connectome representations. In summary, biologically annotated connectomes offer a compelling way to study neural wiring in concert with local biological features.
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Affiliation(s)
- Vincent Bazinet
- Montréal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Justine Y Hansen
- Montréal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Bratislav Misic
- Montréal Neurological Institute, McGill University, Montréal, Quebec, Canada.
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6
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Mehta K, Salo T, Madison T, Adebimpe A, Bassett DS, Bertolero M, Cieslak M, Covitz S, Houghton A, Keller AS, Luo A, Miranda-Dominguez O, Nelson SM, Shafiei G, Shanmugan S, Shinohara RT, Sydnor VJ, Feczko E, Fair DA, Satterthwaite TD. XCP-D: A Robust Pipeline for the post-processing of fMRI data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567926. [PMID: 38045258 PMCID: PMC10690221 DOI: 10.1101/2023.11.20.567926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.
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Affiliation(s)
- Kahini Mehta
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor Salo
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Madison
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Azeez Adebimpe
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Danielle S Bassett
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, PA 19104, USA
- Department of Electrical & Systems Engineering, University of Pennsylvania, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Santa Fe Institute, Santa Fe, NM, 87051, USA
| | - Max Bertolero
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Arielle S Keller
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Audrey Luo
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oscar Miranda-Dominguez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
- Institute of Child Development, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Steve M Nelson
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Golia Shafiei
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sheila Shanmugan
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Valerie J Sydnor
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Feczko
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Damien A Fair
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
- Institute of Child Development, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Sydnor VJ, Larsen B, Seidlitz J, Adebimpe A, Alexander-Bloch AF, Bassett DS, Bertolero MA, Cieslak M, Covitz S, Fan Y, Gur RE, Gur RC, Mackey AP, Moore TM, Roalf DR, Shinohara RT, Satterthwaite TD. Intrinsic activity development unfolds along a sensorimotor-association cortical axis in youth. Nat Neurosci 2023; 26:638-649. [PMID: 36973514 PMCID: PMC10406167 DOI: 10.1038/s41593-023-01282-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/15/2023] [Indexed: 03/29/2023]
Abstract
Animal studies of neurodevelopment have shown that recordings of intrinsic cortical activity evolve from synchronized and high amplitude to sparse and low amplitude as plasticity declines and the cortex matures. Leveraging resting-state functional MRI (fMRI) data from 1,033 youths (ages 8-23 years), we find that this stereotyped refinement of intrinsic activity occurs during human development and provides evidence for a cortical gradient of neurodevelopmental change. Declines in the amplitude of intrinsic fMRI activity were initiated heterochronously across regions and were coupled to the maturation of intracortical myelin, a developmental plasticity regulator. Spatiotemporal variability in regional developmental trajectories was organized along a hierarchical, sensorimotor-association cortical axis from ages 8 to 18. The sensorimotor-association axis furthermore captured variation in associations between youths' neighborhood environments and intrinsic fMRI activity; associations suggest that the effects of environmental disadvantage on the maturing brain diverge most across this axis during midadolescence. These results uncover a hierarchical neurodevelopmental axis and offer insight into the progression of cortical plasticity in humans.
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Affiliation(s)
- Valerie J Sydnor
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bart Larsen
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jakob Seidlitz
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Azeez Adebimpe
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron F Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dani S Bassett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | - Maxwell A Bertolero
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Cieslak
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Covitz
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Fan
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Allyson P Mackey
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | - Tyler M Moore
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David R Roalf
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T Shinohara
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Clement P, Castellaro M, Okell TW, Thomas DL, Vandemaele P, Elgayar S, Oliver-Taylor A, Kirk T, Woods JG, Vos SB, Kuijer JPA, Achten E, van Osch MJP, Detre JA, Lu H, Alsop DC, Chappell MA, Hernandez-Garcia L, Petr J, Mutsaerts HJMM. ASL-BIDS, the brain imaging data structure extension for arterial spin labeling. Sci Data 2022; 9:543. [PMID: 36068231 PMCID: PMC9448788 DOI: 10.1038/s41597-022-01615-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Arterial spin labeling (ASL) is a non-invasive MRI technique that allows for quantitative measurement of cerebral perfusion. Incomplete or inaccurate reporting of acquisition parameters complicates quantification, analysis, and sharing of ASL data, particularly for studies across multiple sites, platforms, and ASL methods. There is a strong need for standardization of ASL data storage, including acquisition metadata. Recently, ASL-BIDS, the BIDS extension for ASL, was developed and released in BIDS 1.5.0. This manuscript provides an overview of the development and design choices of this first ASL-BIDS extension, which is mainly aimed at clinical ASL applications. Discussed are the structure of the ASL data, focussing on storage order of the ASL time series and implementation of calibration approaches, unit scaling, ASL-related BIDS fields, and storage of the labeling plane information. Additionally, an overview of ASL-BIDS compatible conversion and ASL analysis software and ASL example datasets in BIDS format is provided. We anticipate that large-scale adoption of ASL-BIDS will improve the reproducibility of ASL research.
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Affiliation(s)
- Patricia Clement
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
| | - Marco Castellaro
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Thomas W Okell
- Wellcome Centre for Integrative Neuroimaging, FMRIB Division, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - David L Thomas
- Dementia Research Centre, UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK.,Neuroradiological Academic Unit, Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK
| | | | - Sara Elgayar
- Faculty of computers and information science, Ain Shams University, Cairo, Egypt
| | | | - Thomas Kirk
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.,Sir Peter Mansfield Imaging Center, School of Medicine, University of Nottingham, Nottingham, UK
| | - Joseph G Woods
- Wellcome Centre for Integrative Neuroimaging, FMRIB Division, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Center for Functional Magnetic Resonance Imaging, Department of Radiology, University of California San Diego, La Jolla, California, USA
| | - Sjoerd B Vos
- Neuroradiological Academic Unit, Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK.,Centre for Medical Image Computing, University College London, London, UK
| | - Joost P A Kuijer
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Eric Achten
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Matthias J P van Osch
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - John A Detre
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hanzhang Lu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David C Alsop
- Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael A Chappell
- Wellcome Centre for Integrative Neuroimaging, FMRIB Division, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Sir Peter Mansfield Imaging Center, School of Medicine, University of Nottingham, Nottingham, UK.,Radiological Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, UK.,Nottingham Biomedical Research Centre, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | | | - Jan Petr
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands.,Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Henk J M M Mutsaerts
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
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