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Bilgic B, Costagli M, Chan KS, Duyn J, Langkammer C, Lee J, Li X, Liu C, Marques JP, Milovic C, Robinson SD, Schweser F, Shmueli K, Spincemaille P, Straub S, van Zijl P, Wang Y. Recommended implementation of quantitative susceptibility mapping for clinical research in the brain: A consensus of the ISMRM electro-magnetic tissue properties study group. Magn Reson Med 2024; 91:1834-1862. [PMID: 38247051 PMCID: PMC10950544 DOI: 10.1002/mrm.30006] [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: 07/11/2023] [Revised: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
This article provides recommendations for implementing QSM for clinical brain research. It is a consensus of the International Society of Magnetic Resonance in Medicine, Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available have generated a need in the neuroimaging community for guidelines on implementation. This article outlines considerations and implementation recommendations for QSM data acquisition, processing, analysis, and publication. We recommend that data be acquired using a monopolar 3D multi-echo gradient echo (GRE) sequence and that phase images be saved and exported in Digital Imaging and Communications in Medicine (DICOM) format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background field removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields within the brain mask should be removed using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of the whole brain as a region of interest in the analysis. The minimum acquisition and processing details required when reporting QSM results are also provided. These recommendations should facilitate clinical QSM research and promote harmonized data acquisition, analysis, and reporting.
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Affiliation(s)
- Berkin Bilgic
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Mauro Costagli
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Sciences (DINOGMI), University of Genoa, Genoa, Italy
- Laboratory of Medical Physics and Magnetic Resonance, IRCCS Stella Maris, Pisa, Italy
| | - Kwok-Shing Chan
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Jeff Duyn
- Advanced MRI Section, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Jongho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Xu Li
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Chunlei Liu
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - José P Marques
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Carlos Milovic
- School of Electrical Engineering (EIE), Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Simon Daniel Robinson
- High Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
- Centre of Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Ferdinand Schweser
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA
- Center for Biomedical Imaging, Clinical and Translational Science Institute at the University at Buffalo, Buffalo, New York, USA
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Pascal Spincemaille
- MRI Research Institute, Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Sina Straub
- Department of Radiology, Mayo Clinic, Jacksonville, Florida, USA
| | - Peter van Zijl
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Yi Wang
- MRI Research Institute, Departments of Radiology and Biomedical Engineering, Cornell University, New York, New York, USA
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Feng Z, Fan Y, Shi X, Luo X, Xie J, Liu S, Duan C, Wang Q, Ye Y, Yin W. Dysregulation of iron transport-related biomarkers in blood leukocytes is associated with poor prognosis of early trauma. Heliyon 2024; 10:e27000. [PMID: 38463887 PMCID: PMC10923684 DOI: 10.1016/j.heliyon.2024.e27000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/22/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Objective The early targeted and effective diagnosis and treatment of severe trauma are crucial for patients' outcomes. Blood leukocytes act as significant effectors during the initial inflammation and activation of innate immunity in trauma. This study aims to identify hub genes related to patients' prognosis in blood leukocytes at the early stages of trauma. Methods The expression profiles of Gene Expression Omnibus (GEO) Series (GSE) 36809 and GSE11375 were downloaded from the GEO database. R software, GraphPad Prism 9.3.1 software, STRING database, and Cytoscape software were used to process the data and identify hub genes in blood leukocytes of early trauma. Results Gene Ontology (GO) analysis showed that the differentially expressed genes (DEGs) of blood leukocytes at the early stages of trauma (0-4 h, 4-8 h, and 8-12 h) were mainly involved in neutrophil activation and neutrophil degranulation, neutrophil activation involved in immune response, neutrophil mediated immunity, lymphocyte differentiation, and cell killing. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly involved in Osteoclast differentiation and Hematopoietic cell lineage. Sixty-six down-regulated DEGs and 148 up-regulated DEGs were identified and 37 hub genes were confirmed by Molecular Complex Detection (MCODE) of Cytoscape. Among the hub genes, Lipocalin 2 (LCN2), Lactotransferrin (LTF), Olfactomedin 4 (OLFM4), Resistin (RETN), and Transcobalamin 1 (TCN1) were related to prognosis and connected with iron transport closely. LCN2 and LTF were involved in iron transport and had a moderate predictive value for the poor prognosis of trauma patients, and the AUC of LCN2 and LTF was 0.7777 and 0.7843, respectively. Conclusion As iron transport-related hub genes in blood leukocytes, LCN2 and LTF can be used for prognostic prediction of early trauma.
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Affiliation(s)
- Zhusheng Feng
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Yingnan Fan
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Xiaofei Shi
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Xu Luo
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Jiangang Xie
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Shanshou Liu
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Chujun Duan
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Qianmei Wang
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Yuqin Ye
- Department of Neurosurgery, Xijing Hospital, The Air Force Medical University, Xi'an, China
- Department of Neurosurgery, PLA 921th Hospital (Second Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Wen Yin
- Department of Emergency, Xijing Hospital, The Air Force Medical University, Xi'an, China
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Domínguez D JF, Stewart A, Burmester A, Akhlaghi H, O'Brien K, Bollmann S, Caeyenberghs K. Improving quantitative susceptibility mapping for the identification of traumatic brain injury neurodegeneration at the individual level. Z Med Phys 2024:S0939-3889(24)00001-1. [PMID: 38336583 DOI: 10.1016/j.zemedi.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 12/19/2023] [Accepted: 01/07/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Emerging evidence suggests that traumatic brain injury (TBI) is a major risk factor for developing neurodegenerative disease later in life. Quantitative susceptibility mapping (QSM) has been used by an increasing number of studies in investigations of pathophysiological changes in TBI. However, generating artefact-free quantitative susceptibility maps in brains with large focal lesions, as in the case of moderate-to-severe TBI (ms-TBI), is particularly challenging. To address this issue, we utilized a novel two-pass masking technique and reconstruction procedure (two-pass QSM) to generate quantitative susceptibility maps (QSMxT; Stewart et al., 2022, Magn Reson Med.) in combination with the recently developed virtual brain grafting (VBG) procedure for brain repair (Radwan et al., 2021, NeuroImage) to improve automated delineation of brain areas. We used QSMxT and VBG to generate personalised QSM profiles of individual patients with reference to a sample of healthy controls. METHODS Chronic ms-TBI patients (N = 8) and healthy controls (N = 12) underwent (multi-echo) GRE, and anatomical MRI (MPRAGE) on a 3T Siemens PRISMA scanner. We reconstructed the magnetic susceptibility maps using two-pass QSM from QSMxT. We then extracted values of magnetic susceptibility in grey matter (GM) regions (following brain repair via VBG) across the whole brain and determined if they deviate from a reference healthy control group [Z-score < -3.43 or > 3.43, relative to the control mean], with the aim of obtaining personalised QSM profiles. RESULTS Using two-pass QSM, we achieved susceptibility maps with a substantial increase in quality and reduction in artefacts irrespective of the presence of large focal lesions, compared to single-pass QSM. In addition, VBG minimised the loss of GM regions and exclusion of patients due to failures in the region delineation step. Our findings revealed deviations in magnetic susceptibility measures from the HC group that differed across individual TBI patients. These changes included both increases and decreases in magnetic susceptibility values in multiple GM regions across the brain. CONCLUSIONS We illustrate how to obtain magnetic susceptibility values at the individual level and to build personalised QSM profiles in ms-TBI patients. Our approach opens the door for QSM investigations in more severely injured patients. Such profiles are also critical to overcome the inherent heterogeneity of clinical populations, such as ms-TBI, and to characterize the underlying mechanisms of neurodegeneration at the individual level more precisely. Moreover, this new personalised QSM profiling could in the future assist clinicians in assessing recovery and formulating a neuroscience-guided integrative rehabilitation program tailored to individual TBI patients.
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Affiliation(s)
- Juan F Domínguez D
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Geelong, Australia.
| | - Ashley Stewart
- School of Information Technology and Electrical Engineering, Faculty of Engineering, Architecture, and Information Technology, The University of Queensland, Brisbane, Australia
| | - Alex Burmester
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Geelong, Australia
| | - Hamed Akhlaghi
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Geelong, Australia; Department of Emergency Medicine, St. Vincent's Hospital, Melbourne, Australia
| | - Kieran O'Brien
- Siemens Healthcare Pty Ltd, Brisbane, Queensland, Australia
| | - Steffen Bollmann
- School of Information Technology and Electrical Engineering, Faculty of Engineering, Architecture, and Information Technology, The University of Queensland, Brisbane, Australia; Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Karen Caeyenberghs
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Geelong, Australia
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Oka S, Yamaki T, Sasaki M, Ukai R, Takemura M, Yokoyama T, Kataoka-Sasaki Y, Onodera R, Ito YM, Kobayashi S, Kocsis JD, Iwadate Y, Honmou O. Intravenous infusion of auto serum-expanded autologous mesenchymal stem cells in chronic brain injury patients: a study protocol for a Phase II trial (Preprint). JMIR Res Protoc 2022; 11:e37898. [PMID: 35793128 PMCID: PMC9301565 DOI: 10.2196/37898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Objective Methods Results Conclusions Trial Registration International Registered Report Identifier (IRRID)
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Affiliation(s)
- Shinichi Oka
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Advanced Regenerative Therapeutics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomohiro Yamaki
- Division of Neurosurgery, Rehabilitation Center for Traumatic Apallics Chiba, National Agency for Automotive Safety and Victims' Aid, Chiba, Japan
| | - Masanori Sasaki
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Advanced Regenerative Therapeutics, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Ryo Ukai
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mitsuhiro Takemura
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takahiro Yokoyama
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuko Kataoka-Sasaki
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Advanced Regenerative Therapeutics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Rie Onodera
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoichi M Ito
- Data Science Center, Institute of Health Science Innovation for Medical Care, Hokkaido University Hospital, Sapporo, Japan
| | - Shigeki Kobayashi
- Division of Neurosurgery, Rehabilitation Center for Traumatic Apallics Chiba, National Agency for Automotive Safety and Victims' Aid, Chiba, Japan
| | - Jeffery D Kocsis
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, United States
| | - Yasuo Iwadate
- Department of Neurological Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Osamu Honmou
- Department of Neural Regenerative Medicine, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Advanced Regenerative Therapeutics, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
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