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Milovic C, Lambert M, Langkammer C, Bredies K, Irarrazaval P, Tejos C. Streaking artifact suppression of quantitative susceptibility mapping reconstructions via L1-norm data fidelity optimization (L1-QSM). Magn Reson Med 2022; 87:457-473. [PMID: 34350634 DOI: 10.1002/mrm.28957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 01/05/2023]
Abstract
PURPOSE The presence of dipole-inconsistent data due to substantial noise or artifacts causes streaking artifacts in quantitative susceptibility mapping (QSM) reconstructions. Often used Bayesian approaches rely on regularizers, which in turn yield reduced sharpness. To overcome this problem, we present a novel L1-norm data fidelity approach that is robust with respect to outliers, and therefore prevents streaking artifacts. METHODS QSM functionals are solved with linear and nonlinear L1-norm data fidelity terms using functional augmentation, and are compared with equivalent L2-norm methods. Algorithms were tested on synthetic data, with phase inconsistencies added to mimic lesions, QSM Challenge 2.0 data, and in vivo brain images with hemorrhages. RESULTS The nonlinear L1-norm-based approach achieved the best overall error metric scores and better streaking artifact suppression. Notably, L1-norm methods could reconstruct QSM images without using a brain mask, with similar regularization weights for different data fidelity weighting or masking setups. CONCLUSION The proposed L1-approach provides a robust method to prevent streaking artifacts generated by dipole-inconsistent data, renders brain mask calculation unessential, and opens novel challenging clinical applications such asassessing brain hemorrhages and cortical layers.
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Affiliation(s)
- Carlos Milovic
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Mathias Lambert
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | - Christian Langkammer
- Department of Neurology, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Kristian Bredies
- BioTechMed Graz, Graz, Austria
- Institute of Mathematics and Scientific Computing, University of Graz, Graz, Austria
| | - Pablo Irarrazaval
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
- Institute for Biological and Medical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Cristian Tejos
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
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Xie H, Zhuang H, Guo Y, Sharma RD, Zhang Q, Li J, Lu S, Xu L, Chan Q, Yoneda T, Spincemaille P, Zhang H, Guo H, Prince MR, Yu C, Wang Y. The appearance of magnetic susceptibility objects in SWI phase depends on object size: Comparison with QSM and CT. Clin Imaging 2021; 82:67-72. [PMID: 34798560 DOI: 10.1016/j.clinimag.2021.11.005] [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: 07/14/2021] [Revised: 10/14/2021] [Accepted: 11/07/2021] [Indexed: 11/03/2022]
Abstract
PURPOSE Tissue magnetic susceptibility sign can potentially be detected on susceptibility weighted imaging (SWI) phase (SW-P). This study aims to investigate its performance for depicting brain susceptibility structures. METHODS A simulation was performed to depict magnetic susceptibility structures of various geometries on SW-P and quantitative susceptibility mapping (QSM). Brain MRI was performed on 25 subjects using SWI on a 3 T MRI system. QSM was generated from the same data. SW-P and QSM were analyzed according to radiological assessment for depicting globus pallidus nuclei, optic radiation white matter tracts, and lateral ventricular choroid plexus calcifications. In 11 of these subjects, CT was available and correlated with SW-P and QSM to assess their performance in quantifying calcifications in the choroid plexus. RESULTS In simulation, the appearance of a sphere on SW-P ranged from centric nodule to mixed positive and negative values as the diameter increased. Large cylinders also appeared as mixed positive and negative values. In comparison, QSM correctly depicted the susceptibility distribution of all magnetic structures. On human brain images, SW-P depicted the globus pallidus and optic radiation with mixed positive and negative values, consistent with simulation, and small choroid plexus calcifications as either mixed positive and negative values or as centric nodules; QSM depicted all structures as solid structures with the expected signs. For measuring calcification in the choroid plexus, QSM vs CT linear regression had a higher coefficient of determination compared to SW-P vs CT and SW-P vs QSM. CONCLUSION Appearance of susceptibility sources on SW-P changes with object size. This problem can be overcome using QSM.
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Affiliation(s)
- Hong Xie
- Department of Radiology, The First College of Clinical Medical Science, Three Gorges University, Yichang, Hubei Province, China
| | - Hangwei Zhuang
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Yihao Guo
- Department of Biomedical Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Ria D Sharma
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qihao Zhang
- Department of Radiology, Weill Medical College of Cornell University, New York, NY, USA
| | - Jiahao Li
- Department of Radiology, Weill Medical College of Cornell University, New York, NY, USA
| | - Shimin Lu
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Liang Xu
- Department of Radiology, The First College of Clinical Medical Science, Three Gorges University, Yichang, Hubei Province, China
| | | | - Tetsuya Yoneda
- Department of Medical Imaging Sciences, Kumamoto University, Kumamoto, Japan
| | - Pascal Spincemaille
- Department of Radiology, Weill Medical College of Cornell University, New York, NY, USA
| | - Honglei Zhang
- Department of Radiology, Weill Medical College of Cornell University, New York, NY, USA; Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hua Guo
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Martin R Prince
- Department of Radiology, Weill Medical College of Cornell University, New York, NY, USA
| | - Chengxin Yu
- Department of Radiology, The First College of Clinical Medical Science, Three Gorges University, Yichang, Hubei Province, China
| | - Yi Wang
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA; Department of Radiology, Weill Medical College of Cornell University, New York, NY, USA.
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Kan H, Tsuchiya T, Yamada M, Kunitomo H, Kasai H, Shibamoto Y. Delineation of prostatic calcification using quantitative susceptibility mapping: Spatial accuracy for magnetic resonance-only radiotherapy planning. J Appl Clin Med Phys 2021; 23:e13469. [PMID: 34726833 PMCID: PMC8833270 DOI: 10.1002/acm2.13469] [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: 07/29/2021] [Revised: 10/07/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
To investigate the spatial accuracy of delineating prostatic calcifications by quantitative susceptibility mapping (QSM) in comparison with computed tomography (CT), we conducted phantom and human studies. Five differently‐sized spherical hydroxyapatites mimicking prostatic calcification (pseudo‐calcification) were arranged in the order of their sizes at the center of a plastic container filled with gelatin. This calcification phantom underwent magnetic resonance (MR) imaging, including the multiple spoiled gradient‐echo sequences (SPGR) for the QSM and CT as a reference. The volume of each pseudo‐calcification and center‐to‐center distance between the pseudo‐calcifications delineated by QSM and CT were measured. In the human study, eight patients with prostate cancer who underwent radiation therapy and had some prostatic calcifications were included. The patients underwent CT and SPGR and modified DIXON sequence for MR‐only simulation. The hybrid QSM processing combined with the complex signals in the SPGR and water and fat fraction maps estimated from the modified DIXON sequence were used to reconstruct the pelvic susceptibility map in humans. The threshold of CT numbers was set at 130 HU, while the QSM images were manually segmented in the calcification phantom and human studies. In the phantom study, there was an excellent agreement in the pseudo‐calcification volumes between QSM and CT (y = 1.02x – 7.38, R2 = 0.99). The signal profiles had similar trends in CT and QSM. The center‐to‐center distances between the pseudo‐calcifications in the phantom were also identical in QSM and CT. The calcification volumes were almost identical between the QSM and CT in the human study (y = 0.95x – 9.32, R2 = 1.00). QSM can offer geometric and volumetric accuracies to delineate prostatic calcifications, similar to CT. The prostatic calcification delineated by QSM may facilitate image‐guided radiotherapy in the MR‐only simulation workflow.
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Affiliation(s)
- Hirohito Kan
- Department of Integrated Health Sciences, Graduate School of Medicine, Nagoya University, Nagoya, Japan.,Department of Radiology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Takahiro Tsuchiya
- Department of Radiology, Nagoya City University Hospital, Nagoya City University, Nagoya, Japan
| | - Masato Yamada
- Department of Radiology, Nagoya City University Hospital, Nagoya City University, Nagoya, Japan
| | - Hiroshi Kunitomo
- Department of Radiology, Nagoya City University Hospital, Nagoya City University, Nagoya, Japan
| | - Harumasa Kasai
- Department of Radiology, Nagoya City University Hospital, Nagoya City University, Nagoya, Japan
| | - Yuta Shibamoto
- Department of Radiology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
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Fan W, Wang X, Zhang X, Liu M, Meng Q, Chen Z. Investigating Optimal Echo Times for Quantitative Susceptibility Mapping of Basal Ganglia Nuclei in the Healthy Brain. Curr Med Imaging 2021; 16:991-996. [PMID: 33081660 DOI: 10.2174/1573405615666191219102044] [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: 08/03/2019] [Revised: 11/21/2019] [Accepted: 12/02/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Quantitative susceptibility mapping (QSM) technique had been used to measure the magnetic susceptibility of brain tissue in clinical practice. However, QSM presented echo-time (TE) dependence, and an appropriate number of echo-times (nTEs) for QSM became more important to obtain the reliable susceptibility value. OBJECTIVE The aim of the study was to explore the optimal nTEs for quantitative susceptibility mapping (QSM) measurements of basal ganglia nuclei in the healthy brain. METHODS 3D multi-echo enhanced gradient recalled echo T2 star weighted angiography (ESWAN) sequence was acquired on a 3.0T MR scanner for QSM analysis. Regions of interests (ROIs) were drawn along the margin of the head of the caudate nucleus (HCN), putamen (Pu) and globus pallidus (GP). The mean susceptibility value and standard deviation of the ROIs were derived from the pixels within each region. RESULTS CV analysis demonstrated that TE6, TE8 and TE14 ESWAN sequences presented consistent lower CV value (< 1) for QSM measure of HCN, Pu and GP. ANOVA identified that susceptibility value showed no significant difference between TE6 and TE8 in HCN, Pu and GP (P > 0.05). ICC analysis demonstrated that the susceptibility value of TE6-TE8 had the highest ICC value as compared with TE6-TE14 and TE8-TE14 in HCN, Pu and GP. Combined with the timeefficiency of MRI scanning, TE6 sequence could not only provide the reliable QSM measurement but also short imaging time. CONCLUSION The current study identified that the optimal nTEs of ESWAN were 6 TEs (2.9ms ~ 80.9ms) for QSM measurement of basal ganglia nuclei in the healthy brain.
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Affiliation(s)
- Wenping Fan
- Department of Radiology, Hainan Hospital of Chinese PLA General Hospital, Sanya 572013, China
| | - Xue Wang
- Department of Radiology, Hainan Hospital of Chinese PLA General Hospital, Sanya 572013, China
| | - Xingwen Zhang
- Department of Neurology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Mengqi Liu
- Department of Radiology, Hainan Hospital of Chinese PLA General Hospital, Sanya 572013, China,Department of Radiology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Qinglin Meng
- Department of Radiology, Hainan Hospital of Chinese PLA General Hospital, Sanya 572013, China
| | - Zhiye Chen
- Department of Radiology, Hainan Hospital of Chinese PLA General Hospital, Sanya 572013, China,Department of Radiology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
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Li J, Huang W, Luo X, Wen Y, Cho J, Kovanlikaya I, Gauthier SA, Nguyen TD, Spincemaille P, Wang Y. The central vein sign in multiple sclerosis lesions: Susceptibility relaxation optimization from a routine MRI multiecho gradient echo sequence. J Neuroimaging 2021; 32:48-56. [PMID: 34664747 DOI: 10.1111/jon.12938] [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: 04/16/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND AND PURPOSE The white matter lesion central vein sign (CVS) is an emerging biomarker for multiple sclerosis (MS) differential diagnosis. Currently, CVS is detected on susceptibility weighted imaging (SWI) with suboptimal contrast. We developed an imaging method called susceptibility relaxation optimization (SRO) to improve CVS visualization. METHODS This was a retrospective study of MS patients who had MRI in June 2018 with routine 3D multiecho gradient echo (GRE) and T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences. SRO and SWI images were reconstructed from GRE data. MS lesions were identified on FLAIR image. The CVS detection rate, the image quality score of CVS conspicuity (range 0-3), and central vein-to-lesion contrast were compared between SRO and SWI images. RESULTS In 20 MS patients (mean age 45 ± 9 years; 15 women), SRO significantly increased CVS detection rate compared to SWI (53.3%, 274/514 vs. 32.9%, 169/514; p<.001, McNemar's test). The median image quality score for SRO was 2 compared to 1 for SWI (p<.001, Wilcoxon signed-rank test). The median overall image quality score for SRO was 7 compared to 6 for SWI (p = .003; Wilcoxon signed-rank test). Central vein-to-lesion contrast was 0.12 ± 0.12 in SRO compared to 0.031 ± 0.075 in SWI (p<.001, t-test). CONCLUSIONS SRO yields better central vein contrast and increases CVS detection rate compared to SWI.
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Affiliation(s)
- Jiahao Li
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Weiyuan Huang
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Xianfu Luo
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Yan Wen
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Junghun Cho
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Ilhami Kovanlikaya
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Susan A Gauthier
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA.,Brain and Mind Institute, Weill Medical College of Cornell University, New York, New York, USA.,Department of Neurology, Weill Medical College of Cornell University, New York, New York, USA
| | - Thanh D Nguyen
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Pascal Spincemaille
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Yi Wang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
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Isaacs BR, Heijmans M, Kuijf ML, Kubben PL, Ackermans L, Temel Y, Keuken MC, Forstmann BU. Variability in subthalamic nucleus targeting for deep brain stimulation with 3 and 7 Tesla magnetic resonance imaging. NEUROIMAGE-CLINICAL 2021; 32:102829. [PMID: 34560531 PMCID: PMC8463907 DOI: 10.1016/j.nicl.2021.102829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/12/2021] [Accepted: 09/12/2021] [Indexed: 12/13/2022]
Abstract
Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an effective surgical treatment for Parkinson's disease (PD). Side-effects may, however, be induced when the DBS lead is placed suboptimally. Currently, lower field magnetic resonance imaging (MRI) at 1.5 or 3 Tesla (T) is used for targeting. Ultra-high-field MRI (7 T and above) can obtain superior anatomical information and might therefore be better suited for targeting. This study aims to test whether optimized 7 T imaging protocols result in less variable targeting of the STN for DBS compared to clinically utilized 3 T images. Three DBS-experienced neurosurgeons determined the optimal STN DBS target site on three repetitions of 3 T-T2, 7 T-T2*, 7 T-R2* and 7 T-QSM images for five PD patients. The distance in millimetres between the three repetitive coordinates was used as an index of targeting variability and was compared between field strength, MRI contrast and repetition with a Bayesian ANOVA. Further, the target coordinates were registered to MNI space, and anatomical coordinates were compared between field strength, MRI contrast and repetition using a Bayesian ANOVA. The results indicate that the neurosurgeons are stable in selecting the DBS target site across MRI field strength, MRI contrast and repetitions. The analysis of the coordinates in MNI space however revealed that the actual selected location of the electrode is seemingly more ventral when using the 3 T scan compared to the 7 T scans.
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Affiliation(s)
- Bethany R Isaacs
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, Amsterdam, The Netherlands; Translational Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Margot Heijmans
- Translational Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands.
| | - Mark L Kuijf
- Translational Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands; Department of Neurology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Pieter L Kubben
- Translational Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands; Department of Neurosurgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Linda Ackermans
- Translational Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands; Department of Neurosurgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Yasin Temel
- Translational Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands; Department of Neurosurgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Max C Keuken
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, Amsterdam, The Netherlands
| | - Birte U Forstmann
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, Amsterdam, The Netherlands
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Lorio S, Sedlacik J, So PW, Parkes HG, Gunny R, Löbel U, Li YF, Ogunbiyi O, Mistry T, Dixon E, Adler S, Cross JH, Baldeweg T, Jacques TS, Shmueli K, Carmichael DW. Quantitative MRI susceptibility mapping reveals cortical signatures of changes in iron, calcium and zinc in malformations of cortical development in children with drug-resistant epilepsy. Neuroimage 2021; 238:118102. [PMID: 34058334 PMCID: PMC8350142 DOI: 10.1016/j.neuroimage.2021.118102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Malformations of cortical development (MCD), including focal cortical dysplasia (FCD), are the most common cause of drug-resistant focal epilepsy in children. Histopathological lesion characterisation demonstrates abnormal cell types and lamination, alterations in myelin (typically co-localised with iron), and sometimes calcification. Quantitative susceptibility mapping (QSM) is an emerging MRI technique that measures tissue magnetic susceptibility (χ) reflecting it's mineral composition. We used QSM to investigate abnormal tissue composition in a group of children with focal epilepsy with comparison to effective transverse relaxation rate (R2*) and Synchrotron radiation X-ray fluorescence (SRXRF) elemental maps. Our primary hypothesis was that reductions in χ would be found in FCD lesions, resulting from alterations in their iron and calcium content. We also evaluated deep grey matter nuclei for changes in χ with age. METHODS QSM and R2* maps were calculated for 40 paediatric patients with suspected MCD (18 histologically confirmed) and 17 age-matched controls. Patients' sub-groups were defined based on concordant electro-clinical or histopathology data. Quantitative investigation of QSM and R2* was performed within lesions, using a surface-based approach with comparison to homologous regions, and within deep brain regions using a voxel-based approach with regional values modelled with age and epilepsy as covariates. Synchrotron radiation X-ray fluorescence (SRXRF) was performed on brain tissue resected from 4 patients to map changes in iron, calcium and zinc and relate them to MRI parameters. RESULTS Compared to fluid-attenuated inversion recovery (FLAIR) or T1-weighted imaging, QSM improved lesion conspicuity in 5% of patients. In patients with well-localised lesions, quantitative profiling demonstrated decreased χ, but not R2*, across cortical depth with respect to the homologous regions. Contra-lateral homologous regions additionally exhibited increased χ at 2-3 mm cortical depth that was absent in lesions. The iron decrease measured by the SRXRF in FCDIIb lesions was in agreement with myelin reduction observed by Luxol Fast Blue histochemical staining. SRXRF analysis in two FCDIIb tissue samples showed increased zinc and calcium in one patient, and decreased iron in the brain region exhibiting low χ and high R2* in both patients. QSM revealed expected age-related changes in the striatum nuclei, substantia nigra, sub-thalamic and red nucleus. CONCLUSION QSM non-invasively revealed cortical/sub-cortical tissue alterations in MCD lesions and in particular that χ changes in FCDIIb lesions were consistent with reduced iron, co-localised with low myelin and increased calcium and zinc content. These findings suggest that measurements of cortical χ could be used to characterise tissue properties non-invasively in epilepsy lesions.
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Affiliation(s)
- Sara Lorio
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK; Wellcome EPSRC Centre for Medical Engineering, School of Biomedical Engineering and Imaging Sciences, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Jan Sedlacik
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Center for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Po-Wah So
- Department of Neuroimaging, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Harold G Parkes
- Department of Neuroimaging, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Roxana Gunny
- Department of Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ulrike Löbel
- Department of Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Yao-Feng Li
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London and Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Pathology Department, Tri-Service General Hospital and National Defence Medical Centre, Taipei, Taiwan, ROC
| | - Olumide Ogunbiyi
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London and Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Talisa Mistry
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London and Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Emma Dixon
- MRI Group, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Sophie Adler
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - J Helen Cross
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Torsten Baldeweg
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London and Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karin Shmueli
- MRI Group, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - David W Carmichael
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK; Wellcome EPSRC Centre for Medical Engineering, School of Biomedical Engineering and Imaging Sciences, King's College London, St Thomas' Hospital, London SE1 7EH, UK.
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Thomas GEC, Zarkali A, Ryten M, Shmueli K, Gil-Martinez AL, Leyland LA, McColgan P, Acosta-Cabronero J, Lees AJ, Weil RS. Regional brain iron and gene expression provide insights into neurodegeneration in Parkinson's disease. Brain 2021; 144:1787-1798. [PMID: 33704443 PMCID: PMC8320305 DOI: 10.1093/brain/awab084] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
The mechanisms responsible for the selective vulnerability of specific neuronal populations in Parkinson's disease are poorly understood. Oxidative stress secondary to brain iron accumulation is one postulated mechanism. We measured iron deposition in 180 cortical regions of 96 patients with Parkinson's disease and 35 control subjects using quantitative susceptibility mapping. We estimated the expression of 15 745 genes in the same regions using transcriptomic data from the Allen Human Brain Atlas. Using partial least squares regression, we then identified the profile of gene transcription in the healthy brain that underlies increased cortical iron in patients with Parkinson's disease relative to controls. Applying gene ontological tools, we investigated the biological processes and cell types associated with this transcriptomic profile and identified the sets of genes with spatial expression profiles in control brains that correlated significantly with the spatial pattern of cortical iron deposition in Parkinson's disease. Gene ontological analyses revealed that these genes were enriched for biological processes relating to heavy metal detoxification, synaptic function and nervous system development and were predominantly expressed in astrocytes and glutamatergic neurons. Furthermore, we demonstrated that the genes differentially expressed in Parkinson's disease are associated with the pattern of cortical expression identified in this study. Our findings provide mechanistic insights into regional selective vulnerabilities in Parkinson's disease, particularly the processes involving iron accumulation.
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Affiliation(s)
| | | | - Mina Ryten
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1B 5EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, WC1N 1EH, UK
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, WC1N 1EH, UK
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, UCL, London, WC1E 6BT, UK
| | - Ana Luisa Gil-Martinez
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1B 5EH, UK
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, WC1N 1EH, UK
| | | | - Peter McColgan
- Huntington’s Disease Centre, UCL Institute of Neurology, London, WC1B 5EH, UK
| | | | - Andrew J Lees
- Reta Lila Weston Institute of Neurological Studies, London, WC1N 1PJ, UK
| | - Rimona S Weil
- Dementia Research Centre, UCL, London, WC1N 3AR, UK
- Wellcome Centre for Human Neuroimaging, UCL, London, WC1N 3AR, UK
- Movement Disorders Consortium, UCL, London, WC1N 3BG, UK
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Zhu X, Gao Y, Liu F, Crozier S, Sun H. Deep grey matter quantitative susceptibility mapping from small spatial coverages using deep learning. Z Med Phys 2021; 32:188-198. [PMID: 34312047 PMCID: PMC9948866 DOI: 10.1016/j.zemedi.2021.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Quantitative Susceptibility Mapping (QSM) is generally acquired with full brain coverage, even though many QSM brain-iron studies focus on the deep grey matter (DGM) region only. Reducing the spatial coverage to the DGM vicinity can substantially shorten the scan time or enhance the spatial resolution without increasing scan time; however, this may lead to significant DGM susceptibility underestimation. METHOD A recently proposed deep learning-based QSM method, namely xQSM, is investigated to assess the accuracy of dipole inversion on reduced brain coverages. The xQSM method is compared with two conventional dipole inversion methods using simulated and in vivo experiments from 4 healthy subjects at 3T. Pre-processed magnetic field maps are extended symmetrically from the centre of globus pallidus in the coronal plane to simulate QSM acquisitions of difference spatial coverages, ranging from 100% (∼32mm) to 400% (∼128mm) of the actual DGM physical size. RESULTS The proposed xQSM network led to the lowest DGM contrast loss in both simulated and in vivo subjects, with the smallest susceptibility variation range across all spatial coverages. For the digital brain phantom simulation, xQSM improved the DGM susceptibility underestimation more than 20% in small spatial coverages, as compared to conventional methods. For the in vivo acquisition, less than 5% DGM susceptibility error was achieved in 48mm axial slabs using the xQSM network, while a minimum of 112mm coverage was required for conventional methods. It is also shown that the background field removal process performed worse in reduced brain coverages, which further deteriorated the subsequent dipole inversion. CONCLUSION The recently proposed deep learning-based xQSM method significantly improves the accuracy of DGM QSM from small spatial coverages as compared with conventional QSM algorithms, which can shorten DGM QSM acquisition time substantially.
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Affiliation(s)
| | | | | | | | - Hongfu Sun
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Australia.
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Boehm C, Sollmann N, Meineke J, Ruschke S, Dieckmeyer M, Weiss K, Zimmer C, Makowski MR, Baum T, Karampinos DC. Preconditioned water-fat total field inversion: Application to spine quantitative susceptibility mapping. Magn Reson Med 2021; 87:417-430. [PMID: 34255370 DOI: 10.1002/mrm.28903] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 02/05/2023]
Abstract
PURPOSE To (a) develop a preconditioned water-fat total field inversion (wfTFI) algorithm that directly estimates the susceptibility map from complex multi-echo gradient echo data for water-fat regions and to (b) evaluate the performance of the proposed wfTFI quantitative susceptibility mapping (QSM) method in comparison with a local field inversion (LFI) method and a linear total field inversion (TFI) method in the spine. METHODS Numerical simulations and in vivo spine multi-echo gradient echo measurements were performed to compare wfTFI to an algorithm based on disjoint background field removal (BFR) and LFI and to a formerly proposed TFI algorithm. The data from 1 healthy volunteer and 10 patients with metastatic bone disease were included in the analysis. Clinical routine computed tomography (CT) images were used as a reference standard to distinguish osteoblastic from osteolytic changes. The ability of the QSM methods to distinguish osteoblastic from osteolytic changes was evaluated. RESULTS The proposed wfTFI method was able to decrease the normalized root mean square error compared to the LFI and TFI methods in the simulation. The in vivo wfTFI susceptibility maps showed reduced BFR artifacts, noise amplification, and streaking artifacts compared to the LFI and TFI maps. wfTFI provided a significantly higher diagnostic confidence in differentiating osteolytic and osteoblastic lesions in the spine compared to the LFI method (p = .012). CONCLUSION The proposed wfTFI method can minimize BFR artifacts, noise amplification, and streaking artifacts in water-fat regions and can thus better differentiate between osteoblastic and osteolytic changes in patients with metastatic disease compared to LFI and the original TFI method.
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Affiliation(s)
- Christof Boehm
- Department of Diagnostic and Interventional Radiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Nico Sollmann
- 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.,Department of Diagnostic and Interventional Radiology, University Hospital Ulm, Ulm, Germany
| | | | - Stefan Ruschke
- Department of Diagnostic and Interventional Radiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Michael Dieckmeyer
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 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
| | - Marcus R Makowski
- Department of Diagnostic and Interventional Radiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Thomas Baum
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Dimitrios C Karampinos
- Department of Diagnostic and Interventional Radiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
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Marques JP, Meineke J, Milovic C, Bilgic B, Chan K, Hedouin R, van der Zwaag W, Langkammer C, Schweser F. QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures. Magn Reson Med 2021; 86:526-542. [PMID: 33638241 PMCID: PMC8048665 DOI: 10.1002/mrm.28716] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE To create a realistic in silico head phantom for the second QSM reconstruction challenge and for future evaluations of processing algorithms for QSM. METHODS We created a digital whole-head tissue property phantom by segmenting and postprocessing high-resolution (0.64 mm isotropic), multiparametric MRI data acquired at 7 T from a healthy volunteer. We simulated the steady-state magnetization at 7 T using a Bloch simulator and mimicked a Cartesian sampling scheme through Fourier-based processing. Computer code for generating the phantom and performing the MR simulation was designed to facilitate flexible modifications of the phantom in the future, such as the inclusion of pathologies as well as the simulation of a wide range of acquisition protocols. Specifically, the following parameters and effects were implemented: TR and TE, voxel size, background fields, and RF phase biases. Diffusion-weighted imaging phantom data are provided, allowing future investigations of tissue-microstructure effects in phase and QSM algorithms. RESULTS The brain part of the phantom featured realistic morphology with spatial variations in relaxation and susceptibility values similar to the in vivo setting. We demonstrated some of the phantom's properties, including the possibility of generating phase data with nonlinear evolution over TE due to partial-volume effects or complex distributions of frequency shifts within the voxel. CONCLUSION The presented phantom and computer programs are publicly available and may serve as a ground truth in future assessments of the faithfulness of quantitative susceptibility reconstruction algorithms.
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Affiliation(s)
- José P. Marques
- Donders Institute for Brain, Cognition and BehaviorRadboud UniversityNijmegenthe Netherlands
| | | | - Carlos Milovic
- Department of Electrical EngineeringPontificia Universidad Catolica de ChileSantiagoChile
- Biomedical Imaging CenterPontificia Universidad Catolica de ChileSantiagoChile
- Department of Medical Physics and Biomedical EngineeringUniversity College LondonLondonUnited Kingdom
| | - Berkin Bilgic
- Athinoula A. Martinos Center for Biomedical ImagingCharlestownMassachusettsUSA
- Department of RadiologyHarvard Medical SchoolBostonMassachusettsUSA
- Harvard‐MIT Health Sciences and TechnologyMITCambridgeMassachusettsUSA
| | - Kwok‐Shing Chan
- Donders Institute for Brain, Cognition and BehaviorRadboud UniversityNijmegenthe Netherlands
| | - Renaud Hedouin
- Donders Institute for Brain, Cognition and BehaviorRadboud UniversityNijmegenthe Netherlands
- Centre Inria Rennes ‐ Bretagne AtlantiqueRennesFrance
| | | | | | - Ferdinand Schweser
- Buffalo Neuroimaging Analysis CenterDepartment of NeurologyJacobs School of Medicine and Biomedical SciencesUniversity at BuffaloThe State University of New YorkBuffaloNew YorkUSA
- Center for Biomedical Imaging, Clinical and Translational Science InstituteUniversity at BuffaloThe State University of New YorkBuffaloNew YorkUSA
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62
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Chen L, Cai S, van Zijl PC, Li X. Single-step calculation of susceptibility through multiple orientation sampling. NMR IN BIOMEDICINE 2021; 34:e4517. [PMID: 33822416 PMCID: PMC8184590 DOI: 10.1002/nbm.4517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 03/06/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
Quantitative susceptibility mapping (QSM) was developed to estimate the spatial distribution of magnetic susceptibility from MR signal phase acquired using a gradient echo (GRE) sequence. The field-to-susceptibility inversion in QSM is known to be ill-posed and needs numerical stabilization through either regularization or data oversampling. The calculation of susceptibility through the multiple orientation sampling (COSMOS) method uses phase data acquired at three or more head orientations to achieve a well-conditioned field-to-susceptibility inversion and is often considered the gold standard for in vivo QSM. However, the conventional COSMOS approach, here named multistep COSMOS (MSCOSMOS), solves the dipole inversion from the local field derived from raw GRE phase through multiple steps of phase preprocessing. Error propagations between these consecutive phase processing steps can thus affect the final susceptibility quantification. On the other hand, recently proposed single-step QSM (SSQSM) methods aim to solve an integrated inversion from unprocessed or total phase to mitigate such error propagations but have been limited to single orientation QSM. This study therefore aimed to test the feasibility of using single-step COSMOS (SSCOSMOS) to jointly perform background field removal and dipole inversion with multiple orientation sampling, which could serve as a better standard for gauging SSQSM methods. We incorporated multiple spherical mean value (SMV) kernels of various radii with the dipole inversion in SSCOSMOS. QSM reconstructions with SSCOSMOS and MSCOSMOS were compared using both simulations with a numerical head phantom and in vivo human brain data. SSCOSMOS permitted integrated background removal and dipole inversion without the need to adjust any regularization parameters. In addition, with sufficiently large SMV kernels, SSCOSMOS performed consistently better than MSCOSMOS in all the tested error metrics in our simulations, giving better susceptibility quantification and smaller reconstruction error. Consistent tissue susceptibility values were obtained between SSCOSMOS and MSCOSMOS.
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Affiliation(s)
- Lin Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, United States
- Department of Radiology and Radiological Sciences, Johns Hopkins University, Baltimore, Maryland, United States
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Peter C.M. van Zijl
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, United States
- Department of Radiology and Radiological Sciences, Johns Hopkins University, Baltimore, Maryland, United States
| | - Xu Li
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, United States
- Department of Radiology and Radiological Sciences, Johns Hopkins University, Baltimore, Maryland, United States
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63
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Xu M, Guo Y, Cheng J, Xue K, Yang M, Song X, Feng Y, Cheng J. Brain iron assessment in patients with First-episode schizophrenia using quantitative susceptibility mapping. NEUROIMAGE-CLINICAL 2021; 31:102736. [PMID: 34186296 PMCID: PMC8254125 DOI: 10.1016/j.nicl.2021.102736] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/30/2021] [Accepted: 06/17/2021] [Indexed: 11/28/2022]
Abstract
Patients with first-episode schizophrenia had significantly decreased QSM values in the bilateral substantia nigra, left red nucleus and left thalamus. Patients with first-episode schizophrenia had significantly increased regional volumes in the bilateral putamen and bilateral substantia nigra. QSM provides superior sensitivity over R2* mapping in the evaluation of schizophrenia-related iron alterations. QSM values in regions that showed intergroup differences did not exhibited significant correlations with PANSS scores.
Purpose Decreased serum ferritin level was recently found in schizophrenia. Whether the brain iron concentration in schizophrenia exists abnormality is of research significance. Quantitative susceptibility mapping (QSM) was used in this study to assess brain iron changes in the grey matter nuclei of patients with first-episode schizophrenia. Methods The local ethics committee approved the study, and all subjects gave written informed consent. Thirty patients with first-episode schizophrenia and 30 age and gender-matched healthy controls were included in this study. QSM and effective transverse relaxation rate (R2*) maps were reconstructed from a three-dimensional multi-echo gradient-echo sequence. The inter-group differences of regional QSM values, R2* values and volumes were calculated in the grey matter nuclei, including bilateral caudate nucleus, putamen, globus pallidus, substantia nigra, red nucleus, and thalamus. The diagnostic performance of QSM and R2* was evaluated using receiver operating characteristic curve. The correlations between regional iron variations and clinical PANSS (Positive and Negative Syndrome Scale) scores were assessed using partial correlation analysis. Results Compared to healthy controls, patients with first-episode schizophrenia had significantly decreased QSM values (less paramagnetic) in the bilateral substantia nigra, left red nucleus and left thalamus (p < 0.05, FDR correction). QSM proved more sensitive than R2* regarding inter-group differences. The highest diagnostic performance for first-episode schizophrenia was observed in QSM value of the left substantia nigra (area under the curve, AUC = 0.718, p = 0.004). Regional volumes of bilateral putamen and bilateral substantia nigra were increased (p < 0.05, FDR correction) in first-episode schizophrenia. However, both QSM and R2* values did not show significant correlations with PANSS scores (p > 0.05). Conclusion This study reveals decreased iron concentration in grey matter nuclei of patients with first-episode schizophrenia. QSM provides superior sensitivity over R2* in the evaluation of schizophrenia-related brain iron changes. It demonstrated that QSM may be a potential biomarker for further understanding the pathophysiological mechanism of first-episode schizophrenia.
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Affiliation(s)
- Man Xu
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yihao Guo
- MR Collaboration, Siemens Healthcare Ltd, Guangzhou, China
| | - Junying Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kangkang Xue
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng Yang
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xueqin Song
- Department of Psychiatry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanqiu Feng
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Medical Image Processing, Key Laboratory of Mental Health of the Ministry of Education & Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.
| | - Jingliang Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Fortier V, Fortin MA, Pater P, Souhami L, Levesque IR. A role for magnetic susceptibility in synthetic computed tomography. Phys Med 2021; 85:137-146. [PMID: 34004446 DOI: 10.1016/j.ejmp.2021.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Radiotherapy treatment planning based on magnetic resonance imaging (MRI) benefits from increased soft-tissue contrast and functional imaging. MRI-only planning is attractive but limited by the lack of electron density information required for dose calculation, and the difficulty to differentiate air and bone. MRI can map magnetic susceptibility to separate bone from air. A method is introduced to produce synthetic CT (sCT) through automatic voxel-wise assignment of CT numbers from an MRI dataset processed that includes magnetic susceptibility mapping. METHODS Volumetric multi-echo gradient echo datasets were acquired in the heads of five healthy volunteers and fourteen patients with cancer using a 3 T MRI system. An algorithm for CT synthesis was designed using the volunteer data, based on fuzzy c-means clustering and adaptive thresholding of the MR data (magnitude, fat, water, and magnetic susceptibility). Susceptibility mapping was performed using a modified version of the iterative phase replacement algorithm. On patient data, the algorithm was assessed by direct comparison to X-ray computed tomography (CT) scans. RESULTS The skull, spine, teeth, and major sinuses were clearly distinguished in all sCT, from healthy volunteers and patients. The mean absolute CT number error between X-ray CT and sCT in patients ranged from 78 and 134 HU. CONCLUSION Susceptibility mapping using MRI can differentiate air and bone for CT synthesis. The proposed method is automated, fast, and based on a commercially available MRI pulse sequence. The method avoids registration errors and does not rely on a priori information, making it suitable for nonstandard anatomy.
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Affiliation(s)
- Véronique Fortier
- Medical Physics Unit, McGill University, Montréal, QC, Canada; Biomedical Engineering, McGill University, Montréal, QC, Canada.
| | | | - Piotr Pater
- Medical Physics Unit, McGill University, Montréal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada
| | - Luis Souhami
- Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada; Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Ives R Levesque
- Medical Physics Unit, McGill University, Montréal, QC, Canada; Biomedical Engineering, McGill University, Montréal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada; Research Institute of the McGill University Health Centre, Montréal, QC, Canada
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65
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Chen Z, Chen Z. Computed inverse MRI (CIMRI) for intrinsic brain magnetic susceptibility mapping. Comput Biol Med 2021; 134:104498. [PMID: 34051451 DOI: 10.1016/j.compbiomed.2021.104498] [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: 03/12/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/24/2022]
Abstract
In magnetic resonance imaging (MRI), tissue magnetization in the main field B0 is a necessary preparation for magnetic resonance signal formation that imposes an inherent dipole effect on MRI signals, which predisposes an artifact on tissue MRI. In the MRI principle, T2*-weighted MRI can be described by a cascade of data transformations: from the source of tissue magnetic susceptibility (denoted by χ) to the output of complex-valued T2* image (in a magnitude and phase pair). Under the linear approximation of the T2* phase MRI, we can computationally reconstruct the source χ by quantitative susceptibility mapping (QSM), which is an inverse solution that is modeled by computed inverse MRI (CIMRI). For a brain function study using MRI (fMRI), we can reconstruct a timeseries of brain χ images to represent the intrinsic brain function activity called functional QSM (fQSM). This intrinsic depiction is defined as the removal of the artifactual dipole effect and other MRI-introduced distortions from phase data through inverse mapping. With one high-resolution QSM experiment and one group (20 subjects) low-resolution fQSM experiment, we show that the dipole effect manifests as ripples around vessels and a spatial split at a local activation blob and that the dipole effect could be removed by CIMRI. In the context of inverse imaging or undoing MRI transformations (including dipole convolution), we computationally achieve brain intrinsic structural depiction by QSM and intrinsic functional depiction by fQSM.
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Affiliation(s)
- Zeyuan Chen
- Department of Computer Sciences, University of California-Davis, Davis, CA, 95616, USA.
| | - Zikuan Chen
- Department of Diagnostic Radiology, City of Hope National Medical Center, Duarte, CA, 91010, USA; Zinv LLC, Albuquerque, NM, 87108, USA.
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Lindemeyer J, Worthoff WA, Shymanskaya A, Shah NJ. Iterative Restoration of the Fringe Phase (REFRASE) for QSM. Front Neurosci 2021; 15:537666. [PMID: 34054401 PMCID: PMC8155380 DOI: 10.3389/fnins.2021.537666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/01/2021] [Indexed: 12/03/2022] Open
Abstract
In quantitative susceptibility mapping (QSM), reconstructed results can be critically biased by misinterpreted or missing phase data near the edges of the brain support originating from the non-local relationship between field and susceptibility. These data either have to be excluded or corrected before further processing can take place. To address this, our iterative restoration of the fringe phase (REFRASE) approach simultaneously enhances the accuracy of multi-echo phase data QSM maps and the extent of the area available for evaluation. Data loss caused by strong local phase gradients near the surface of the brain support is recovered within the original phase data using harmonic and dipole-based fields extrapolated from a robust support region toward an extended brain mask. Over several iterations, phase data are rectified prior to the application of further QSM processing steps. The concept is successfully validated on numerical phantoms and brain scans from a cohort of volunteers. The increased extent of the mask and improved numerical stability within the segmented globus pallidus confirm the efficacy of the presented method in comparison to traditional evaluation.
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Affiliation(s)
- Johannes Lindemeyer
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany
| | - Wieland A Worthoff
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany
| | | | - N Jon Shah
- Institute of Neuroscience and Medicine-4, Forschungszentrum Jülich, Jülich, Germany.,Institute of Neuroscience and Medicine-11, Forschungszentrum Jülich, Jülich, Germany.,JARA-BRAIN-Translational Medicine, Aachen, Germany.,Department of Neurology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
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Biondetti E, Santin MD, Valabrègue R, Mangone G, Gaurav R, Pyatigorskaya N, Hutchison M, Yahia-Cherif L, Villain N, Habert MO, Arnulf I, Leu-Semenescu S, Dodet P, Vila M, Corvol JC, Vidailhet M, Lehéricy S. The spatiotemporal changes in dopamine, neuromelanin and iron characterizing Parkinson's disease. Brain 2021; 144:3114-3125. [PMID: 33978742 PMCID: PMC8634084 DOI: 10.1093/brain/awab191] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
In Parkinson's disease, there is a progressive reduction in striatal dopaminergic function, and loss of neuromelanin-containing dopaminergic neurons and increased iron deposition in the substantia nigra. We tested the hypothesis of a relationship between impairment of the dopaminergic system and changes in the iron metabolism. Based on imaging data of patients with prodromal and early clinical Parkinson's disease, we assessed the spatiotemporal ordering of such changes and relationships in the sensorimotor, associative and limbic territories of the nigrostriatal system. Patients with Parkinson's disease (disease duration < 4 years) or idiopathic REM sleep behaviour disorder (a prodromal form of Parkinson's disease) and healthy controls underwent longitudinal examination (baseline and 2-year follow-up). Neuromelanin and iron sensitive MRI and dopamine transporter single-photon emission tomography were performed to assess nigrostriatal levels of neuromelanin, iron, and dopamine. For all three functional territories of the nigrostriatal system, in the clinically most and least affected hemispheres separately, the following was performed: cross-sectional and longitudinal inter-group difference analysis of striatal dopamine and iron, and nigral neuromelanin and iron; in Parkinson's disease patients, exponential fitting analysis to assess the duration of the prodromal phase and the temporal ordering of changes in dopamine, neuromelanin or iron relative to controls; voxel-wise correlation analysis to investigate concomitant spatial changes in dopamine-iron, dopamine-neuromelanin and neuromelanin-iron in the substantia nigra pars compacta. The temporal ordering of dopaminergic changes followed the known spatial pattern of progression involving first the sensorimotor, then the associative and limbic striatal and nigral regions. Striatal dopaminergic denervation occurred first followed by abnormal iron metabolism and finally neuromelanin changes in the substantia nigra pars compacta, which followed the same spatial and temporal gradient observed in the striatum but shifted in time. In conclusion, dopaminergic striatal dysfunction and cell loss in the substantia nigra pars compacta are interrelated with increased nigral iron content.
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Affiliation(s)
- Emma Biondetti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Centre de NeuroImagerie de Recherche - CENIR, 75013 Paris, France.,ICM, Team "Movement Investigations and Therapeutics" (MOV'IT), 75013 Paris, France
| | - Mathieu D Santin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Centre de NeuroImagerie de Recherche - CENIR, 75013 Paris, France
| | - Romain Valabrègue
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Centre de NeuroImagerie de Recherche - CENIR, 75013 Paris, France
| | - Graziella Mangone
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neurology, Centre d'Investigation Clinique Neurosciences, 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neurology, 75013 Paris, France
| | - Rahul Gaurav
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Centre de NeuroImagerie de Recherche - CENIR, 75013 Paris, France.,ICM, Team "Movement Investigations and Therapeutics" (MOV'IT), 75013 Paris, France
| | - Nadya Pyatigorskaya
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Team "Movement Investigations and Therapeutics" (MOV'IT), 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neuroradiology, 75013 Paris, France
| | | | - Lydia Yahia-Cherif
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Centre de NeuroImagerie de Recherche - CENIR, 75013 Paris, France
| | - Nicolas Villain
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neurology, 75013 Paris, France
| | - Marie-Odile Habert
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Nuclear Medicine, 75013 Paris, France.,Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale - LIB, 75006 Paris, France
| | - Isabelle Arnulf
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Team "Movement Investigations and Therapeutics" (MOV'IT), 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Sleep Disorder Unit, 75013 Paris, France
| | - Smaranda Leu-Semenescu
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Sleep Disorder Unit, 75013 Paris, France
| | - Pauline Dodet
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Sleep Disorder Unit, 75013 Paris, France
| | - Miquel Vila
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED)-Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona (UAB)-Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Jean-Christophe Corvol
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neurology, Centre d'Investigation Clinique Neurosciences, 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neurology, 75013 Paris, France
| | - Marie Vidailhet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Team "Movement Investigations and Therapeutics" (MOV'IT), 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neurology, 75013 Paris, France
| | - Stéphane Lehéricy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, 75013 Paris, France.,ICM, Centre de NeuroImagerie de Recherche - CENIR, 75013 Paris, France.,ICM, Team "Movement Investigations and Therapeutics" (MOV'IT), 75013 Paris, France.,Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Department of Neuroradiology, 75013 Paris, France
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Rotta J, Perosa V, Yakupov R, Kuijf HJ, Schreiber F, Dobisch L, Oltmer J, Assmann A, Speck O, Heinze HJ, Acosta-Cabronero J, Duzel E, Schreiber S. Detection of Cerebral Microbleeds With Venous Connection at 7-Tesla MRI. Neurology 2021; 96:e2048-e2057. [PMID: 33653897 DOI: 10.1212/wnl.0000000000011790] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/28/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Cerebral microbleeds (MBs) are a common finding in patients with cerebral small vessel disease (CSVD) and Alzheimer disease as well as in healthy elderly people, but their pathophysiology remains unclear. To investigate a possible role of veins in the development of MBs, we performed an exploratory study, assessing in vivo presence of MBs with a direct connection to a vein. METHODS 7-Tesla (7T) MRI was conducted and MBs were counted on quantitative susceptibility mapping (QSM). A submillimeter resolution QSM-based venogram allowed identification of MBs with a direct spatial connection to a vein. RESULTS A total of 51 people (mean age [SD] 70.5 [8.6] years, 37% female) participated in the study: 20 had CSVD (cerebral amyloid angiopathy [CAA] with strictly lobar MBs [n = 8], hypertensive arteriopathy [HA] with strictly deep MBs [n = 5], or mixed lobar and deep MBs [n = 7], 72.4 [6.1] years, 30% female) and 31 were healthy controls (69.4 [9.9] years, 42% female). In our cohort, we counted a total of 96 MBs with a venous connection, representing 14% of all detected MBs on 7T QSM. Most venous MBs (86%, n = 83) were observed in lobar locations and all of these were cortical. Patients with CAA showed the highest ratio of venous to total MBs (19%) (HA = 9%, mixed = 18%, controls = 5%). CONCLUSION Our findings establish a link between cerebral MBs and the venous vasculature, pointing towards a possible contribution of veins to CSVD in general and to CAA in particular. Pathologic studies are needed to confirm our observations.
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Affiliation(s)
- Johanna Rotta
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Valentina Perosa
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK.
| | - Renat Yakupov
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Hugo J Kuijf
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Frank Schreiber
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Laura Dobisch
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Jan Oltmer
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Anne Assmann
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Oliver Speck
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Hans-Jochen Heinze
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Julio Acosta-Cabronero
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Emrah Duzel
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
| | - Stefanie Schreiber
- From the Department of Neurology (J.R., V.P., F.S., A.A., H.-J.H., S.S.) and Institute of Physics (O.S.), Otto-von-Guericke University; Institute of Cognitive Neurology and Dementia Research (IKND) (V.P., R.Y., J.O., H.-J.H., E.D.), Magdeburg, Germany; J. Philip Kistler Stroke Research Center (V.P.), Massachusetts General Hospital, Boston; German Center for Neurodegenerative Diseases (DZNE) (R.Y., F.S., L.D., O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Image Sciences Institute (H.J.K.), University Medical Center Utrecht, the Netherlands; Leibniz-Institute for Neurobiology (LIN) (O.S., H.-J.H., E.D.); Center for Behavioral Brain Sciences (CBBS) (O.S., H.-J.H., E.D., S.S.), Magdeburg, Germany; Tenoke Limited (J.A.-C.), Cambridge, UK; and Institute of Cognitive Neuroscience (E.D.), University College London, UK
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Gao Y, Zhu X, Moffat BA, Glarin R, Wilman AH, Pike GB, Crozier S, Liu F, Sun H. xQSM: quantitative susceptibility mapping with octave convolutional and noise-regularized neural networks. NMR IN BIOMEDICINE 2021; 34:e4461. [PMID: 33368705 DOI: 10.1002/nbm.4461] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Quantitative susceptibility mapping (QSM) provides a valuable MRI contrast mechanism that has demonstrated broad clinical applications. However, the image reconstruction of QSM is challenging due to its ill-posed dipole inversion process. In this study, a new deep learning method for QSM reconstruction, namely xQSM, was designed by introducing noise regularization and modified octave convolutional layers into a U-net backbone and trained with synthetic and in vivo datasets, respectively. The xQSM method was compared with two recent deep learning (QSMnet+ and DeepQSM) and two conventional dipole inversion (MEDI and iLSQR) methods, using both digital simulations and in vivo experiments. Reconstruction error metrics, including peak signal-to-noise ratio, structural similarity, normalized root mean squared error and deep gray matter susceptibility measurements, were evaluated for comparison of the different methods. The results showed that the proposed xQSM network trained with in vivo datasets achieved the best reconstructions of all the deep learning methods. In particular, it led to, on average, 32.3%, 25.4% and 11.7% improvement in the accuracy of globus pallidus susceptibility estimation for digital simulations and 39.3%, 21.8% and 6.3% improvements for in vivo acquisitions compared with DeepQSM, QSMnet+ and iLSQR, respectively. It also exhibited the highest linearity against different susceptibility intensity scales and demonstrated the most robust generalization capability to various spatial resolutions of all the deep learning methods. In addition, the xQSM method also substantially shortened the reconstruction time from minutes using MEDI to only a few seconds.
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Affiliation(s)
- Yang Gao
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Australia
| | - Xuanyu Zhu
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Australia
| | - Bradford A Moffat
- Melbourne Brain Centre Imaging Unit, Department of Medicine and Radiology, The University of Melbourne, Parkville, Australia
| | - Rebecca Glarin
- Melbourne Brain Centre Imaging Unit, Department of Medicine and Radiology, The University of Melbourne, Parkville, Australia
- Department of Radiology, Royal Melbourne Hospital, Parkville, Australia
| | - Alan H Wilman
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada
| | - G Bruce Pike
- Departments of Radiology and Clinical Neurosciences, University of Calgary, Calgary, Canada
| | - Stuart Crozier
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Australia
| | - Feng Liu
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Australia
| | - Hongfu Sun
- School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Australia
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Dimov AV, Christoforidis GA, Saadat N, Liu MM, Jeong YI, Roth S, Niekrasz M, Carroll TJ. QSM in canine model of acute cerebral ischemia: A pilot study. Magn Reson Med 2021; 85:1602-1610. [PMID: 33034078 DOI: 10.1002/mrm.28498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/28/2020] [Accepted: 08/05/2020] [Indexed: 11/07/2022]
Abstract
PURPOSE In the present study, we investigated the potential of QSM to assess the physiological state of cortical tissue in the middle cerebral artery occlusion canine model of a cerebral ischemia. METHODS Experiments were performed in 8 anesthetized canines. Gradient echo, perfusion, and DWI data of brains at normal and ischemic states were acquired. In the postprocessed susceptibility and quantitative cerebral blood flow maps, changes in values within the middle cerebral artery-fed cortical territories were quantified both on the ischemic and normal contralateral hemisphere side. RESULTS QSM values in critically ischemic tissue were significantly different from contralateral values-namely, susceptibility increase was observed in the cases in which cerebral perfusion was maintained above the threshold of neuronal death. Furthermore, the data indicates presence of a significant correlation between the changes in susceptibility values, cerebral perfusion, and the infarct volume and pial collateral scores. Additionally, our data suggests that difference in cortical susceptibility is prospectively indicative of the infarct growth rate. CONCLUSION In an experimental permanent middle cerebral artery occlusion model, QSM was shown to correlate with the functional parameters characterizing viability of ischemic tissue, thus warranting further research on its ability to provide complementary information during acute stroke MRI examinations in humans.
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Affiliation(s)
- Alexey V Dimov
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
| | | | - Niloufar Saadat
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
| | - Mira M Liu
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
| | - Yong I Jeong
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
| | - Steven Roth
- Department of Anesthesiology, University of Illinois, College of Medicine, Chicago, Illinois, USA
| | - Marek Niekrasz
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Timothy J Carroll
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
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Susceptibility Weighted Imaging for evaluation of musculoskeletal lesions. Eur J Radiol 2021; 138:109611. [PMID: 33677418 DOI: 10.1016/j.ejrad.2021.109611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 11/23/2022]
Abstract
The presence of blood or calcium in the musculoskeletal (MSK) system may be linked to specific pathological conditions. The ability of MRI for calcium detection is usually limited compared with other techniques such as CT. In a similar manner, the accuracy of MRI for detection and evaluation of hemorrhage in soft tissues is closely linked to the degree of degradation of blood products. Blood and calcium are substances that cause local inhomogeneity of the magnetic field resulting in susceptibility artifacts. To try to evaluate these substances, specific MRI sequences which are highly sensitive to these local magnetic field inhomogeneities such as Susceptibility Weighted Imaging (SWI) have been developed and successfully applied in the Central Nervous System, but scarcely used in MSK. SWI may increase the overall sensitivity of MRI to detect blood and calcium in several clinical scenarios such as degenerative joint disease or bone and soft tissue lesion assessment and discriminate between both compounds, something which is not always possible with conventional MRI approaches. In this paper, physical basis and technical adjustment for SWI acquisition at MSK are detailed reviewing the potential application of SWI in different MSK clinical scenarios.
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Voelker MN, Kraff O, Goerke S, Laun FB, Hanspach J, Pine KJ, Ehses P, Zaiss M, Liebert A, Straub S, Eckstein K, Robinson S, Nagel AN, Stefanescu MR, Wollrab A, Klix S, Felder J, Hock M, Bosch D, Weiskopf N, Speck O, Ladd ME, Quick HH. The traveling heads 2.0: Multicenter reproducibility of quantitative imaging methods at 7 Tesla. Neuroimage 2021; 232:117910. [PMID: 33647497 DOI: 10.1016/j.neuroimage.2021.117910] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/25/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
OBJECT This study evaluates inter-site and intra-site reproducibility at ten different 7 T sites for quantitative brain imaging. MATERIAL AND METHODS Two subjects - termed the "traveling heads" - were imaged at ten different 7 T sites with a harmonized quantitative brain MR imaging protocol. In conjunction with the system calibration, MP2RAGE, QSM, CEST and multi-parametric mapping/relaxometry were examined. RESULTS Quantitative measurements with MP2RAGE showed very high reproducibility across sites and subjects, and errors were in concordance with previous results and other field strengths. QSM had high inter-site reproducibility for relevant subcortical volumes. CEST imaging revealed systematic differences between the sites, but reproducibility was comparable to results in the literature. Relaxometry had also very high agreement between sites, but due to the high sensitivity, differences caused by different applications of the B1 calibration of the two RF coil types used were observed. CONCLUSION Our results show that quantitative brain imaging can be performed with high reproducibility at 7 T and with similar reliability as found at 3 T for multicenter studies of the supratentorial brain.
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Affiliation(s)
- Maximilian N Voelker
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| | - Oliver Kraff
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany
| | - Steffen Goerke
- Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederik B Laun
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jannis Hanspach
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Kerrin J Pine
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Moritz Zaiss
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Andrzej Liebert
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sina Straub
- Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Korbinian Eckstein
- High Field MR Center, Department for Biomedical Imaging and Image guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Simon Robinson
- High Field MR Center, Department for Biomedical Imaging and Image guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Armin N Nagel
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maria R Stefanescu
- Chair of Cellular and Molecular Imaging, Comprehensive Heart Failure Center (CHFC), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Astrid Wollrab
- Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Sabrina Klix
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max-Delbrueck-Center for Molecular Medicine, Berlin-Buch, Germany
| | - Jörg Felder
- Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Michael Hock
- Chair of Cellular and Molecular Imaging, Comprehensive Heart Failure Center (CHFC), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Dario Bosch
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
| | - Oliver Speck
- Otto-von-Guericke-University Magdeburg, Magdeburg, Germany; Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Mark E Ladd
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany; Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and Faculty of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Harald H Quick
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany; High-Field and Hybrid MR Imaging, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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Lee H, Lee MJ, Kim EJ, Huh GY, Lee JH, Cho H. Iron accumulation in the oculomotor nerve of the progressive supranuclear palsy brain. Sci Rep 2021; 11:2950. [PMID: 33536537 PMCID: PMC7859181 DOI: 10.1038/s41598-021-82469-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
Abnormal iron accumulation around the substantia nigra (SN) is a diagnostic indicator of Parkinsonism. This study aimed to identify iron-related microarchitectural changes around the SN of brains with progressive supranuclear palsy (PSP) via postmortem validations and in vivo magnetic resonance imaging (MRI). 7 T high-resolution MRI was applied to two postmortem brain tissues, from one normal brain and one PSP brain. Histopathological examinations were performed to demonstrate the molecular origin of the high-resolution postmortem MRI findings, by using ferric iron staining, myelin staining, and two-dimensional laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging. In vivo iron-related MRI was performed on five healthy controls, five patients with Parkinson’s disease (PD), and five patients with PSP. In the postmortem examination, excessive iron deposition along the myelinated fiber at the anterior SN and third cranial nerve (oculomotor nerve) fascicles of the PSP brain was verified by LA-ICP-MS. This region corresponded to those with high R2* values and positive susceptibility from quantitative susceptibility mapping (QSM), but was less sensitive in Perls’ Prussian blue staining. In in vivo susceptibility-weighted imaging, hypointense pixels were observed in the region between the SN and red nucleus (RN) in patients with PSP, but not in healthy controls and patients with PD. R2* and QSM values of such region were significantly higher in patients with PSP compared to those in healthy controls and patients with PD as well (vs. healthy control: p = 0.008; vs. PD: p = 0.008). Thus, excessive iron accumulation along the myelinated fibers at the anterior SN and oculomotor nerve fascicles may be a pathological characteristic and crucial MR biomarker in a brain with PSP.
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Affiliation(s)
- Hansol Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50, UNIST-Gil, Eonyang-eup, Ulju-gun, Ulsan, South Korea
| | - Myung Jun Lee
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Eun-Joo Kim
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Gi Yeong Huh
- Department of Forensic Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Jae-Hyeok Lee
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, 20, Geumo-ro, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do, South Korea.
| | - HyungJoon Cho
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50, UNIST-Gil, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
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74
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Chan KS, Marques JP. SEPIA-Susceptibility mapping pipeline tool for phase images. Neuroimage 2020; 227:117611. [PMID: 33309901 DOI: 10.1016/j.neuroimage.2020.117611] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/14/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022] Open
Abstract
Quantitative susceptibility mapping (QSM) is a physics-driven computational technique that has a high sensitivity in quantifying iron deposition based on MRI phase images. Furthermore, it has a unique ability to distinguish paramagnetic and diamagnetic contributions such as haemorrhage and calcification based on image contrast. These properties have contributed to a growing interest to use QSM not only in research but also in clinical applications. However, it is challenging to obtain high quality susceptibility map because of its ill-posed nature, especially for researchers who have less experience with QSM and the optimisation of its pipeline. In this paper, we present an open-source processing pipeline tool called SuscEptibility mapping PIpeline tool for phAse images (SEPIA) dedicated to the post-processing of MRI phase images and QSM. SEPIA connects various QSM toolboxes freely available in the field to offer greater flexibility in QSM processing. It also provides an interactive graphical user interface to construct and execute a QSM processing pipeline, simplifying the workflow in QSM research. The extendable design of SEPIA also allows developers to deploy their methods in the framework, providing a platform for developers and researchers to share and utilise the state-of-the-art methods in QSM.
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Affiliation(s)
- Kwok-Shing Chan
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands.
| | - José P Marques
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
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75
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Polak D, Chatnuntawech I, Yoon J, Iyer SS, Milovic C, Lee J, Bachert P, Adalsteinsson E, Setsompop K, Bilgic B. Nonlinear dipole inversion (NDI) enables robust quantitative susceptibility mapping (QSM). NMR IN BIOMEDICINE 2020; 33:e4271. [PMID: 32078756 PMCID: PMC7528217 DOI: 10.1002/nbm.4271] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 05/04/2023]
Abstract
High-quality Quantitative Susceptibility Mapping (QSM) with Nonlinear Dipole Inversion (NDI) is developed with pre-determined regularization while matching the image quality of state-of-the-art reconstruction techniques and avoiding over-smoothing that these techniques often suffer from. NDI is flexible enough to allow for reconstruction from an arbitrary number of head orientations and outperforms COSMOS even when using as few as 1-direction data. This is made possible by a nonlinear forward-model that uses the magnitude as an effective prior, for which we derived a simple gradient descent update rule. We synergistically combine this physics-model with a Variational Network (VN) to leverage the power of deep learning in the VaNDI algorithm. This technique adopts the simple gradient descent rule from NDI and learns the network parameters during training, hence requires no additional parameter tuning. Further, we evaluate NDI at 7 T using highly accelerated Wave-CAIPI acquisitions at 0.5 mm isotropic resolution and demonstrate high-quality QSM from as few as 2-direction data.
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Affiliation(s)
- Daniel Polak
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
- Department of Radiology, A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Siemens Healthcare GmbH, Erlangen, Germany
| | - Itthi Chatnuntawech
- National Science and Technology Development Agency, National Nanotechnology Center, Pathum Thani, Thailand
| | - Jaeyeon Yoon
- Laboratory for Imaging Science and Technology, Department of Electrical and Computer Engineering, Seoul National University, Seoul, South Korea
| | - Siddharth Srinivasan Iyer
- Department of Radiology, A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Electronical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Carlos Milovic
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jongho Lee
- Laboratory for Imaging Science and Technology, Department of Electrical and Computer Engineering, Seoul National University, Seoul, South Korea
| | - Peter Bachert
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
- Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elfar Adalsteinsson
- Department of Electronical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kawin Setsompop
- Department of Radiology, A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Berkin Bilgic
- Department of Radiology, A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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76
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Karsa A, Punwani S, Shmueli K. An optimized and highly repeatable MRI acquisition and processing pipeline for quantitative susceptibility mapping in the head-and-neck region. Magn Reson Med 2020; 84:3206-3222. [PMID: 32621302 DOI: 10.1002/mrm.28377] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/06/2020] [Accepted: 05/23/2020] [Indexed: 02/11/2024]
Abstract
PURPOSE Quantitative Susceptibility Mapping (QSM) is an emerging technique sensitive to disease-related changes including oxygenation. It is extensively used in brain studies and has increasing clinical applications outside the brain. Here we present the first MRI acquisition protocol and QSM pipeline optimized for the head-and-neck region together with a repeatability analysis performed in healthy volunteers. METHODS We investigated both the intrasession and the intersession repeatability of the optimized method in 10 subjects. We also implemented two, Tikhonov-regularisation-based susceptibility calculation techniques that were found to have higher contrast-to-noise than existing methods in the head-and-neck region. Repeatability was evaluated by calculating the distributions of susceptibility differences between repeated scans and the corresponding minimum detectable effect sizes (MDEs). RESULTS Deep brain regions had higher QSM repeatability than neck regions. As expected, intrasession repeatability was generally better than intersession repeatability. Susceptibility maps calculated using projection onto dipole fields for background field removal were more repeatable than using the Laplacian boundary value method in the head-and-neck region. Small (short-axis diameter <5 mm) lymph nodes had the lowest repeatability (MDE = 0.27 ppm) as imperfect segmentation included some of the surrounding paramagnetic fatty fascia, highlighting the importance of accurate region delineation. MDEs in the larger lymph nodes (0.16 ppm), submandibular glands (0.10 ppm), and especially the parotid glands (0.06 ppm) were much lower, comparable to those of the brain regions. CONCLUSIONS The high repeatability of the acquisition and pipeline optimized for QSM will facilitate clinical studies in the head-and-neck region.
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Affiliation(s)
- Anita Karsa
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Centre for Medical Imaging, University College London, London, United Kingdom
| | - Shonit Punwani
- Centre for Medical Imaging, University College London, London, United Kingdom
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Centre for Medical Imaging, University College London, London, United Kingdom
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Bechler E, Stabinska J, Thiel T, Jasse J, Zukovs R, Valentin B, Wittsack HJ, Ljimani A. Feasibility of quantitative susceptibility mapping (QSM) of the human kidney. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2020; 34:389-397. [PMID: 33230656 PMCID: PMC8492554 DOI: 10.1007/s10334-020-00895-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 11/28/2022]
Abstract
Objective To evaluate the feasibility of in-vivo quantitative susceptibility mapping (QSM) of the human kidney. Methods An axial single-breath-hold 3D multi-echo sequence (acquisition time 33 s) was completed on a 3 T-MRI-scanner (Magnetom Prisma, Siemens Healthineers, Erlangen, Germany) in 19 healthy volunteers. Graph-cut-based unwrapping combined with the T2*-IDEAL approach was performed to remove the chemical shift of fat and to quantify QSM of the upper abdomen. Mean susceptibility values of the entire, renal cortex and medulla in both kidneys and the liver were determined and compared. Five subjects were measured twice to examine the reproducibility. One patient with severe renal fibrosis was included in the study to evaluate the potential clinical relevance of QSM. Results QSM was successful in 17 volunteers and the patient with renal fibrosis. Anatomical structures in the abdomen were clearly distinguishable by QSM and the susceptibility values obtained in the liver were comparable to those found in the literature. The results showed a good reproducibility. Besides, the mean renal QSM values obtained in healthy volunteers (0.04 ± 0.07 ppm for the right and − 0.06 ± 0.19 ppm for the left kidney) were substantially higher than that measured in the investigated fibrotic kidney (− 0.43 ± − 0.02 ppm). Conclusion QSM of the human kidney could be a promising approach for the assessment of information about microscopic renal tissue structure. Therefore, it might further improve functional renal MR imaging. Electronic supplementary material The online version of this article (10.1007/s10334-020-00895-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eric Bechler
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Julia Stabinska
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Thomas Thiel
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jonas Jasse
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Romans Zukovs
- Department of Haematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Birte Valentin
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Hans-Jörg Wittsack
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Alexandra Ljimani
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
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78
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Wang C, Foxley S, Ansorge O, Bangerter-Christensen S, Chiew M, Leonte A, Menke RA, Mollink J, Pallebage-Gamarallage M, Turner MR, Miller KL, Tendler BC. Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T applied to amyotrophic lateral sclerosis. Neuroimage 2020; 222:117216. [PMID: 32745677 PMCID: PMC7775972 DOI: 10.1016/j.neuroimage.2020.117216] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Susceptibility weighted magnetic resonance imaging (MRI) is sensitive to the local concentration of iron and myelin. Here, we describe a robust image processing pipeline for quantitative susceptibility mapping (QSM) and R2* mapping of fixed post-mortem, whole-brain data. Using this pipeline, we compare the resulting quantitative maps in brains from patients with amyotrophic lateral sclerosis (ALS) and controls, with validation against iron and myelin histology. Twelve post-mortem brains were scanned with a multi-echo gradient echo sequence at 7T, from which susceptibility and R2* maps were generated. Semi-quantitative histological analysis for ferritin (the principal iron storage protein) and myelin proteolipid protein was performed in the primary motor, anterior cingulate and visual cortices. Magnetic susceptibility and R2* values in primary motor cortex were higher in ALS compared to control brains. Magnetic susceptibility and R2* showed positive correlations with both myelin and ferritin estimates from histology. Four out of nine ALS brains exhibited clearly visible hyperintense susceptibility and R2* values in the primary motor cortex. Our results demonstrate the potential for MRI-histology studies in whole, fixed post-mortem brains to investigate the biophysical source of susceptibility weighted MRI signals in neurodegenerative diseases like ALS.
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Affiliation(s)
- Chaoyue Wang
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom.
| | - Sean Foxley
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom; Department of Radiology, University of Chicago, United States
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
| | - Sarah Bangerter-Christensen
- Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom; Brigham Young University, Provo, United States
| | - Mark Chiew
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom
| | - Anna Leonte
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom; University of Groningen,the Netherlands
| | - Ricarda Al Menke
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom
| | - Jeroen Mollink
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom; Department of Anatomy, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, the Netherlands
| | | | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom; Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
| | - Karla L Miller
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom
| | - Benjamin C Tendler
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, United Kingdom
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79
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Boyacioglu R, Wang C, Ma D, McGivney DF, Yu X, Griswold MA. 3D magnetic resonance fingerprinting with quadratic RF phase. Magn Reson Med 2020; 85:2084-2094. [PMID: 33179822 DOI: 10.1002/mrm.28581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 12/26/2022]
Abstract
PURPOSE To implement 3D magnetic resonance fingerprinting (MRF) with quadratic RF phase (qRF-MRF) for simultaneous quantification of T1 , T2 , ΔB0 , and T 2 ∗ . METHODS 3D MRF data with effective undersampling factor of 3 in the slice direction were acquired with quadratic RF phase patterns for T1 , T2 , and T 2 ∗ sensitivity. Quadratic RF phase encodes the off-resonance by modulating the on-resonance frequency linearly in time. Transition to 3D brings practical limitations for reconstruction and dictionary matching because of increased data and dictionary sizes. Randomized singular value decomposition (rSVD)-based compression in time and reduction in dictionary size with a quadratic interpolation method are combined to be able to process prohibitively large data sets in feasible reconstruction and matching times. RESULTS Accuracy of 3D qRF-MRF maps in various resolutions and orientations are compared to 3D fast imaging with steady-state precession (FISP) for T1 and T2 contrast and to 2D qRF-MRF for T 2 ∗ contrast and ΔB0 . The precision of 3D qRF-MRF was 1.5-2 times higher than routine clinical scans. 3D qRF-MRF ΔB0 maps were further processed to highlight the susceptibility contrast. CONCLUSION Natively co-registered 3D whole brain T1 , T2 , T 2 ∗ , ΔB0 , and QSM maps can be acquired in as short as 5 min with 3D qRF-MRF.
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Affiliation(s)
- Rasim Boyacioglu
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Charlie Wang
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dan Ma
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Debra F McGivney
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xin Yu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark A Griswold
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
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80
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Boehm C, Diefenbach MN, Makowski MR, Karampinos DC. Improved body quantitative susceptibility mapping by using a variable-layer single-min-cut graph-cut for field-mapping. Magn Reson Med 2020; 85:1697-1712. [PMID: 33151604 DOI: 10.1002/mrm.28515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE To develop a robust algorithm for field-mapping in the presence of water-fat components, large B 0 field inhomogeneities and MR signal voids and to apply the developed method in body applications of quantitative susceptibility mapping (QSM). METHODS A framework solving the cost-function of the water-fat separation problem in a single-min-cut graph-cut based on the variable-layer graph construction concept was developed. The developed framework was applied to a numerical phantom enclosing an MR signal void, an air bubble experimental phantom, 14 large field of view (FOV) head/neck region in vivo scans and to 6 lumbar spine in vivo scans. Field-mapping and subsequent QSM results using the proposed algorithm were compared to results using an iterative graph-cut algorithm and a formerly proposed single-min-cut graph-cut. RESULTS The proposed method was shown to yield accurate field-map and susceptibility values in all simulation and in vivo datasets when compared to reference values (simulation) or literature values (in vivo). The proposed method showed improved field-map and susceptibility results compared to iterative graph-cut field-mapping especially in regions with low SNR, strong field-map variations and high R 2 ∗ values. CONCLUSIONS A single-min-cut graph-cut field-mapping method with a variable-layer construction was developed for field-mapping in body water-fat regions, improving quantitative susceptibility mapping particularly in areas close to MR signal voids.
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Affiliation(s)
- Christof Boehm
- Department of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany
| | - Maximilian N Diefenbach
- Department of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany.,Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Marcus R Makowski
- Department of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany
| | - Dimitrios C Karampinos
- Department of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany
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81
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Chen J, Cai T, Li Y, Chi J, Rong S, He C, Li X, Zhang P, Wang L, Zhang Y. Different iron deposition patterns in Parkinson's disease subtypes: a quantitative susceptibility mapping study. Quant Imaging Med Surg 2020; 10:2168-2176. [PMID: 33139996 DOI: 10.21037/qims-20-285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Background Parkinson's disease (PD) is a heterogeneous neurodegenerative disorder with various subtypes and uncertain pathogenesis. Iron deposition is considered to be involved in the pathological mechanisms of PD. The present study aimed to investigate the iron deposition in deep gray matter in patients with different PD subtypes using quantitative susceptibility mapping (QSM). Methods Forty-six PD patients and 22 healthy controls (HCs) were recruited for the study. PD patients were allocated to the tremor-dominant (TD) group (n=22), postural instability and gait disorder-dominant (PIGD) group (n=19), and intermediate group (n=5). Susceptibility values in deep gray matter nuclei measured by QSM among the PD-TD and PD-PIGD groups and the HCs, as well as the relationship between iron accumulation and clinical motor features, were investigated. Results Susceptibility values in the dentate nucleus (DN) were greater in the PD-TD (118.73±70.45) group than in the PD-PIGD (72.14±39.85, P=0.02) group and HCs (78.26±41.38, P=0.042). Further, a significant positive correlation was observed between the DN susceptibility values and tremor scores (r=0.324, P=0.028). Compared with the HCs (182.60±85.35), both the PD-TD (282.00±102.49, P=0.006) and PD-PIGD groups (284.91±118.54, P=0.007) exhibited greater susceptibility values in the substantia nigra (SN) pars reticulata. The susceptibility values in the SN pars compacta were also greater in the PD-PIGD group (164.51±89.44) than in the HCs (107.78±63.11, P=0.048). Conclusions The present study demonstrated various iron deposition patterns in different PD phenotypes. These findings give insight into the pathophysiology underlying different PD phenotypes, and potentially illustrate the involvement of iron deposition in the PD-TD and PD-PIGD subtypes.
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Affiliation(s)
- Junling Chen
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Neurology, Shantou Central Hospital, Shantou, China
| | - Tongtong Cai
- Department of Neurology, Shantou Central Hospital, Shantou, China
| | - Yan Li
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jieshan Chi
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Siming Rong
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chentao He
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaohong Li
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Piao Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lijuan Wang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yuhu Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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82
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Isaacs BR, Keuken MC, Alkemade A, Temel Y, Bazin PL, Forstmann BU. Methodological Considerations for Neuroimaging in Deep Brain Stimulation of the Subthalamic Nucleus in Parkinson's Disease Patients. J Clin Med 2020; 9:E3124. [PMID: 32992558 PMCID: PMC7600568 DOI: 10.3390/jcm9103124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Deep brain stimulation (DBS) of the subthalamic nucleus is a neurosurgical intervention for Parkinson's disease patients who no longer appropriately respond to drug treatments. A small fraction of patients will fail to respond to DBS, develop psychiatric and cognitive side-effects, or incur surgery-related complications such as infections and hemorrhagic events. In these cases, DBS may require recalibration, reimplantation, or removal. These negative responses to treatment can partly be attributed to suboptimal pre-operative planning procedures via direct targeting through low-field and low-resolution magnetic resonance imaging (MRI). One solution for increasing the success and efficacy of DBS is to optimize preoperative planning procedures via sophisticated neuroimaging techniques such as high-resolution MRI and higher field strengths to improve visualization of DBS targets and vasculature. We discuss targeting approaches, MRI acquisition, parameters, and post-acquisition analyses. Additionally, we highlight a number of approaches including the use of ultra-high field (UHF) MRI to overcome limitations of standard settings. There is a trade-off between spatial resolution, motion artifacts, and acquisition time, which could potentially be dissolved through the use of UHF-MRI. Image registration, correction, and post-processing techniques may require combined expertise of traditional radiologists, clinicians, and fundamental researchers. The optimization of pre-operative planning with MRI can therefore be best achieved through direct collaboration between researchers and clinicians.
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Affiliation(s)
- Bethany R. Isaacs
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, 1018 WS Amsterdam, The Netherlands; (A.A.); (P.-L.B.); (B.U.F.)
- Department of Experimental Neurosurgery, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands;
| | - Max C. Keuken
- Municipality of Amsterdam, Services & Data, Cluster Social, 1000 AE Amsterdam, The Netherlands;
| | - Anneke Alkemade
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, 1018 WS Amsterdam, The Netherlands; (A.A.); (P.-L.B.); (B.U.F.)
| | - Yasin Temel
- Department of Experimental Neurosurgery, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands;
| | - Pierre-Louis Bazin
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, 1018 WS Amsterdam, The Netherlands; (A.A.); (P.-L.B.); (B.U.F.)
- Max Planck Institute for Human Cognitive and Brain Sciences, D-04103 Leipzig, Germany
| | - Birte U. Forstmann
- Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam, 1018 WS Amsterdam, The Netherlands; (A.A.); (P.-L.B.); (B.U.F.)
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Multi-centre, multi-vendor reproducibility of 7T QSM and R 2* in the human brain: Results from the UK7T study. Neuroimage 2020; 223:117358. [PMID: 32916289 PMCID: PMC7480266 DOI: 10.1016/j.neuroimage.2020.117358] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/03/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction We present the reliability of ultra-high field T2* MRI at 7T, as part of the UK7T Network's “Travelling Heads” study. T2*-weighted MRI images can be processed to produce quantitative susceptibility maps (QSM) and R2* maps. These reflect iron and myelin concentrations, which are altered in many pathophysiological processes. The relaxation parameters of human brain tissue are such that R2* mapping and QSM show particularly strong gains in contrast-to-noise ratio at ultra-high field (7T) vs clinical field strengths (1.5–3T). We aimed to determine the inter-subject and inter-site reproducibility of QSM and R2* mapping at 7T, in readiness for future multi-site clinical studies. Methods Ten healthy volunteers were scanned with harmonised single- and multi-echo T2*-weighted gradient echo pulse sequences. Participants were scanned five times at each “home” site and once at each of four other sites. The five sites had 1× Philips, 2× Siemens Magnetom, and 2× Siemens Terra scanners. QSM and R2* maps were computed with the Multi-Scale Dipole Inversion (MSDI) algorithm (https://github.com/fil-physics/Publication-Code). Results were assessed in relevant subcortical and cortical regions of interest (ROIs) defined manually or by the MNI152 standard space. Results and Discussion Mean susceptibility (χ) and R2* values agreed broadly with literature values in all ROIs. The inter-site within-subject standard deviation was 0.001–0.005 ppm (χ) and 0.0005–0.001 ms−1 (R2*). For χ this is 2.1–4.8 fold better than 3T reports, and 1.1–3.4 fold better for R2*. The median ICC from within- and cross-site R2* data was 0.98 and 0.91, respectively. Multi-echo QSM had greater variability vs single-echo QSM especially in areas with large B0 inhomogeneity such as the inferior frontal cortex. Across sites, R2* values were more consistent than QSM in subcortical structures due to differences in B0-shimming. On a between-subject level, our measured χ and R2* cross-site variance is comparable to within-site variance in the literature, suggesting that it is reasonable to pool data across sites using our harmonised protocol. Conclusion The harmonized UK7T protocol and pipeline delivers on average a 3-fold improvement in the coefficient of reproducibility for QSM and R2* at 7T compared to previous reports of multi-site reproducibility at 3T. These protocols are ready for use in multi-site clinical studies at 7T.
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Milovic C, Tejos C, Acosta-Cabronero J, Özbay PS, Schwesser F, Marques JP, Irarrazaval P, Bilgic B, Langkammer C. The 2016 QSM Challenge: Lessons learned and considerations for a future challenge design. Magn Reson Med 2020; 84:1624-1637. [PMID: 32086836 PMCID: PMC7526054 DOI: 10.1002/mrm.28185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/09/2019] [Accepted: 01/06/2020] [Indexed: 11/06/2022]
Abstract
PURPOSE The 4th International Workshop on MRI Phase Contrast and QSM (2016, Graz, Austria) hosted the first QSM Challenge. A single-orientation gradient recalled echo acquisition was provided, along with COSMOS and the χ33 STI component as ground truths. The submitted solutions differed more than expected depending on the error metric used for optimization and were generally over-regularized. This raised (unanswered) questions about the ground truths and the metrics utilized. METHODS We investigated the influence of background field remnants by applying additional filters. We also estimated the anisotropic contributions from the STI tensor to the apparent susceptibility to amend the χ33 ground truth and to investigate the impact on the reconstructions. Lastly, we used forward simulations from the COSMOS reconstruction to investigate the impact noise had on the metric scores. RESULTS Reconstructions compared against the amended STI ground truth returned lower errors. We show that the background field remnants had a minor impact in the errors. In the absence of inconsistencies, all metrics converged to the same regularization weights, whereas structural similarity index metric was more insensitive to such inconsistencies. CONCLUSION There was a mismatch between the provided data and the ground truths due to the presence of unaccounted anisotropic susceptibility contributions and noise. Given the lack of reliable ground truths when using in vivo acquisitions, simulations are suggested for future QSM Challenges.
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Affiliation(s)
- Carlos Milovic
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | - Cristian Tejos
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | | | - Pinar Senay Özbay
- Laboratory of Functional and Molecular Imaging, National Institutes of Health, Bethesda, MD, USA
| | - Ferdinand Schwesser
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo, The State University of New York, NY, USA
- Center for Biomedical Imaging, Clinical and Translational Science Institute, University at Buffalo, The State University of New York, NY, USA
| | - Jose Pedro Marques
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Pablo Irarrazaval
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
- Institute for Biological and Medical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Berkin Bilgic
- Martinos Center for Biomedical Imaging, Harvard Medical School, MA, USA
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Kan H, Uchida Y, Arai N, Takizawa M, Miyati T, Kunitomo H, Kasai H, Shibamoto Y. Decreasing iron susceptibility with temperature in quantitative susceptibility mapping: A phantom study. Magn Reson Imaging 2020; 73:55-61. [PMID: 32853756 DOI: 10.1016/j.mri.2020.08.012] [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: 03/12/2020] [Revised: 07/03/2020] [Accepted: 08/20/2020] [Indexed: 01/04/2023]
Abstract
To clarify the temperature dependence of susceptibility estimated by quantitative susceptibility mapping (QSM) analysis, we investigated the relationship between temperature and susceptibility using a cylinder phantom with varying temperatures. Six solutions with various concentrations of superparamagnetic iron oxide (SPIO) nanoparticles were employed. These tubes were placed in a cylinder phantom and surrounded with water. The temperature of the circulated water was adjusted to change the temperature in the cylinder phantom from 25.8 °C to 42.5 °C. The cylinder phantom was scanned via a three-dimensional multiple spoiled gradient-echo sequence for R2* and QSM analyses with varying temperatures. The relationships between temperature, susceptibility, and R2* values were determined. Moreover, the temperature coefficients of susceptibility (χ-Tc) and (R2*-Tc) were calculated at each concentration and the linearities in these indices against each SPIO concentration were validated. Significant inverse correlations were found between temperature, susceptibility, and R2* values at each SPIO concentration due to the decrease in paramagnetic iron susceptibility that occurred with increasing temperature based on Curie's law. Moreover, although there were significant correlations between the susceptibility and R2* values at any temperature, the slopes of the regression lines grew in height with greater temperatures. The percentage of difference per Celsius degree in susceptibility in any SPIO concentration was lower than the corresponding finding among the R2* results. There were strong linearities between the SPIO concentration, χ-Tc (r = -0.994; p < 0.001), and R2*-Tc (r = -0.998; p < 0.001). The χ-Tc and R2*-Tc outcomes in a particular voxel varied considerably with the iron contents. Although there was an inverse correlation noted between temperature and susceptibility, the susceptibility analysis showed smaller temperature dependence relative to the R2* analysis. QSM analysis might be a more suitable option for magnetic resonance-based iron quantification in comparison with R2* relaxometry.
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Affiliation(s)
- Hirohito Kan
- Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20, Daiko-Minami, Higashi-ku, Nagoya, Aichi 461-8673, Japan; Department of Radiology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-ku, Nagoya, Aichi 467-8601, Japan.
| | - Yuto Uchida
- Department of Neurology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-ku, Nagoya, Aichi 467-8601, Japan; Department of Neurology, Toyokawa City Hospital, 23 noji, Yahata-cho, Toyokawa, Aichi 442-8561, Japan
| | - Nobuyuki Arai
- Department of Radiology, Nagoya City University Hospital, 1 Kawasumi, Mizuho-ku, Nagoya, Aichi 467-8601, Japan.
| | - Masahiro Takizawa
- Healthcare Business Unit, Hitachi Ltd., 2-16-1 Higashi-Ueno, Daito-ku, Tokyo 110-0015, Japan.
| | - Tosiaki Miyati
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan.
| | - Hiroshi Kunitomo
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan.
| | - Harumasa Kasai
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Yuta Shibamoto
- Department of Radiology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-ku, Nagoya, Aichi 467-8601, Japan.
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86
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Guo R, Zhao Y, Li Y, Wang T, Li Y, Sutton B, Liang ZP. Simultaneous QSM and metabolic imaging of the brain using SPICE: Further improvements in data acquisition and processing. Magn Reson Med 2020; 85:970-977. [PMID: 32810319 DOI: 10.1002/mrm.28459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/09/2020] [Accepted: 07/12/2020] [Indexed: 01/23/2023]
Abstract
PURPOSE To achieve high-resolution mapping of brain tissue susceptibility in simultaneous QSM and metabolic imaging. METHODS Simultaneous QSM and metabolic imaging was first achieved using SPICE (spectroscopic imaging by exploiting spatiospectral correlation), but the QSM maps thus obtained were at relatively low-resolution (2.0 × 3.0 × 3.0 mm3 ). We overcome this limitation using an improved SPICE data acquisition method with the following novel features: 1) sampling (k, t)-space in dual densities, 2) sampling central k-space fully to achieve nominal spatial resolution of 3.0 × 3.0 × 3.0 mm3 for metabolic imaging, and 3) sampling outer k-space sparsely to achieve spatial resolution of 1.0 × 1.0 × 1.9 mm3 for QSM. To keep the scan time short, we acquired spatiospectral encodings in echo-planar spectroscopic imaging trajectories in central k-space but in CAIPIRINHA (controlled aliasing in parallel imaging results in higher acceleration) trajectories in outer k-space using blipped phase encodings. For data processing and image reconstruction, a union-of-subspaces model was used, effectively incorporating sensitivity encoding, spatial priors, and spectral priors of individual molecules. RESULTS In vivo experiments were carried out to evaluate the feasibility and potential of the proposed method. In a 6-min scan, QSM maps at 1.0 × 1.0 × 1.9 mm3 resolution and metabolic maps at 3.0 × 3.0 × 3.0 mm3 nominal resolution were obtained simultaneously. Compared with the original method, the QSM maps obtained using the new method reveal fine-scale brain structures more clearly. CONCLUSION We demonstrated the feasibility of achieving high-resolution QSM simultaneously with metabolic imaging using a modified SPICE acquisition method. The improved capability of SPICE may further enhance its practical utility in brain mapping.
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Affiliation(s)
- Rong Guo
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yibo Zhao
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yudu Li
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Tianyao Wang
- Department of Radiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, People's Republic of China
| | - Yao Li
- Institute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Brad Sutton
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Zhi-Pei Liang
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
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87
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Cho J, Ma Y, Spincemaille P, Pike GB, Wang Y. Cerebral oxygen extraction fraction: Comparison of dual-gas challenge calibrated BOLD with CBF and challenge-free gradient echo QSM+qBOLD. Magn Reson Med 2020; 85:953-961. [PMID: 32783233 DOI: 10.1002/mrm.28447] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/23/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE To compare cortical gray matter oxygen extraction fraction (OEF) estimated from 2 MRI methods: (1) the quantitative susceptibility mapping (QSM) plus quantitative blood oxygen level dependent imaging (qBOLD) (QSM+qBOLD or QQ), and (2) the dual-gas calibrated-BOLD (DGCB) in healthy subjects; and to investigate the validity of iso-cerebral metabolic rate of oxygen consumption assumption during hypercapnia using QQ. METHODS In 10 healthy subjects, 3 tesla MRI including a multi-echo gradient echo sequence at baseline and hypercapnia for QQ, as well as an EPI dual-echo pseudo-continuous arterial spin labeling for DGCB, were performed under a hypercapnic and a hyperoxic condition. OEFs from QQ and DGCB were compared using region of interest analysis and paired t test. For QQ, cerebral metabolic rate of oxygen consumption = cerebral blood flow*OEF*arterial oxygen content was generated for both baseline and hypercapnia, which were compared. RESULTS Average OEF in cortical gray matter across 10 subjects from QQ versus DGCB was 35.5 ± 6.7% versus 38.0 ± 9.1% (P = .49) at baseline and 20.7 ± 4.4% versus 28.4 ± 7.6% (P = .02) in hypercapnia: OEF in cortical gray matter was significantly reduced as measured in QQ (P < .01) and in DGCB (P < .01). Cerebral metabolic rate of oxygen consumption (in μmol O2 /min/100 g) was 168.2 ± 54.1 at baseline from DGCB and was 153.1 ± 33.8 at baseline and 126.4 ± 34.2 (P < .01) in hypercapnia from QQ. CONCLUSION The differences in OEF obtained from QQ and DGCB are small and nonsignificant at baseline but are statistically significant during hypercapnia. In addition, QQ shows a cerebral metabolic rate of oxygen consumption decrease (17.4%) during hypercapnia.
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Affiliation(s)
- Junghun Cho
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Yuhan Ma
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Pascal Spincemaille
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Gilbert Bruce Pike
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.,Department of Radiology and Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Yi Wang
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA.,Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA
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88
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Li G, Wu R, Tong R, Bo B, Zhao Y, Gillen KM, Spincemaille P, Ku Y, Du Y, Wang Y, Wang X, Li J. Quantitative Measurement of Metal Accumulation in Brain of Patients With Wilson's Disease. Mov Disord 2020; 35:1787-1795. [PMID: 32681698 DOI: 10.1002/mds.28141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Currently, no study has evaluated metal accumulation in the brains of patients with Wilson's disease by using quantitative susceptibility mapping at 3T MRI. The objectives of this study were to qualitatively and quantitatively evaluate changes in magnetic susceptibility and R2* maps in deep gray matter nuclei to discriminate Wilson's disease patients from healthy controls and to evaluate their sensitivities in diagnosing Wilson's disease. METHODS Magnetic susceptibility and R2* maps and conventional T1-weighted, T2-weighted, and T2-weighted fluid-attenuated inversion recovery images were obtained from 17 Wilson's disease patients and 14 age-matched healthy controls on a 3T MRI scanner. Differences between Wilson's disease and healthy control groups in susceptibility and R2* values in multiple deep nuclei were evaluated using a Mann-Whitney U test and receiver operating characteristic curves. The correlations of susceptibility and R2* values with Unified Wilson's Disease Rating Scale score were also performed. RESULTS Magnetic susceptibility and R2* can effectively distinguish different types of signal abnormalities. Magnetic susceptibility and R2* values in multiple deep nuclei of Wilson's disease patients were significantly higher than those in healthy controls. Magnetic susceptibility value in the substantia nigra had the highest area under the curve (0.888). There were positive correlations of the Unified Wilson's Disease Rating Scale score with susceptibility values in the caudate nucleus (r = 0.757, P = 0.011), putamen (r = 0.679, P = 0.031), and red nucleus (r = 0.638, P = 0.047), as well as R2* values in the caudate nucleus (r = 0.754, P = 0.012). CONCLUSIONS Quantitative susceptibility mapping at 3T could be a useful tool to evaluate metal accumulation in deep gray matter nuclei of Wilson's disease patients. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Gaiying Li
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, Shanghai, China
| | - Rong Wu
- Department of Neurology, Shanghai Tong-Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Tong
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, Shanghai, China
| | - Binshi Bo
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, Shanghai, China
| | - Yu Zhao
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, Shanghai, China
| | - Kelly M Gillen
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Pascal Spincemaille
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Yixuan Ku
- Department of Psychology, Sun Yat-sen University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Yasong Du
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Wang
- Department of Radiology, Weill Medical College of Cornell University, New York, New York, USA
| | - Xiaoping Wang
- Department of Neurology, Shanghai Tong-Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianqi Li
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, Shanghai, China
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89
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Biondetti E, Karsa A, Thomas DL, Shmueli K. Investigating the accuracy and precision of TE-dependent versus multi-echo QSM using Laplacian-based methods at 3 T. Magn Reson Med 2020; 84:3040-3053. [PMID: 32491224 DOI: 10.1002/mrm.28331] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/19/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE Multi-echo gradient-recalled echo acquisitions for QSM enable optimizing the SNR for several tissue types through multi-echo (TE) combination or investigating temporal variations in the susceptibility (potentially reflecting tissue microstructure) by calculating one QSM image at each TE (TE-dependent QSM). In contrast with multi-echo QSM, applying Laplacian-based methods (LBMs) for phase unwrapping and background field removal to single TEs could introduce nonlinear temporal variations (independent of tissue microstructure) into the measured susceptibility. Here, we aimed to compare the effect of LBMs on the QSM susceptibilities in TE-dependent versus multi-echo QSM. METHODS TE-dependent recalled echo data simulated in a numerical head phantom and gradient-recalled echo images acquired at 3 T in 10 healthy volunteers. Several QSM pipelines were tested, including four distinct LBMs: sophisticated harmonic artifact reduction for phase data (SHARP), variable-radius sophisticated harmonic artifact reduction for phase data (V-SHARP), Laplacian boundary value background field removal (LBV), and one-step total generalized variation (TGV). Results from distinct pipelines were compared using visual inspection, summary statistics of susceptibility in deep gray matter/white matter/venous regions of interest, and, in the healthy volunteers, regional susceptibility bias analysis and nonparametric tests. RESULTS Multi-echo versus TE-dependent QSM had higher regional accuracy, especially in high-susceptibility regions and at shorter TEs. Everywhere except in the veins, a processing pipeline incorporating TGV provided the most temporally stable TE-dependent QSM results with an accuracy similar to multi-echo QSM. CONCLUSIONS For TE-dependent QSM, carefully choosing LBMs can minimize the introduction of LBM-related nonlinear temporal susceptibility variations.
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Affiliation(s)
- Emma Biondetti
- Centre de NeuroImagerie de Recherche (CENIR), Team "Movement Investigations and Therapeutics", Institut du Cerveau (ICM), Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Paris, France.,Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Anita Karsa
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - David L Thomas
- Dementia Research Centre, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.,Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
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90
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Wu M, Mulder HT, Baron P, Coello E, Menzel MI, van Rhoon GC, Haase A. Correction of motion-induced susceptibility artifacts and B 0 drift during proton resonance frequency shift-based MR thermometry in the pelvis with background field removal methods. Magn Reson Med 2020; 84:2495-2511. [PMID: 32367530 PMCID: PMC7402020 DOI: 10.1002/mrm.28302] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022]
Abstract
Purpose The linear change of the water proton resonance frequency shift (PRFS) with temperature is used to monitor temperature change based on the temporal difference of image phase. Here, the effect of motion‐induced susceptibility artifacts on the phase difference was studied in the context of mild radio frequency hyperthermia in the pelvis. Methods First, the respiratory‐induced field variations were disentangled from digestive gas motion in the pelvis. The projection onto dipole fields (PDF) as well as the Laplacian boundary value (LBV) algorithm were applied on the phase difference data to eliminate motion‐induced susceptibility artifacts. Both background field removal (BFR) algorithms were studied using simulations of susceptibility artifacts, a phantom heating experiment, and volunteer and patient heating data. Results Respiratory‐induced field variations were negligible in the presence of the filled water bolus. Even though LBV and PDF showed comparable results for most data, LBV seemed more robust in our data sets. Some data sets suggested that PDF tends to overestimate the background field, thus removing phase attributed to temperature. The BFR methods even corrected for susceptibility variations induced by a subvoxel displacement of the phantom. The method yielded successful artifact correction in 2 out of 4 patient treatment data sets during the entire treatment duration of mild RF heating of cervical cancer. The heating pattern corresponded well with temperature probe data. Conclusion The application of background field removal methods in PRFS‐based MR thermometry has great potential in various heating applications and body regions to reduce motion‐induced susceptibility artifacts that originate outside the region of interest, while conserving temperature‐induced PRFS. In addition, BFR automatically removes up to a first‐order spatial B0 drift.
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Affiliation(s)
- Mingming Wu
- Munich School of Bioengineering, TUM Department of Physics, Technical University of Munich, Garching, Germany
| | | | - Paul Baron
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eduardo Coello
- Munich School of Bioengineering, TUM Department of Physics, Technical University of Munich, Garching, Germany.,GE Healthcare, Munich, Germany
| | | | | | - Axel Haase
- Munich School of Bioengineering, TUM Department of Physics, Technical University of Munich, Garching, Germany
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Kan H, Uchida Y, Arai N, Ueki Y, Aoki T, Kasai H, Kunitomo H, Hirose Y, Matsukawa N, Shibamoto Y. Simultaneous voxel-based magnetic susceptibility and morphometry analysis using magnetization-prepared spoiled turbo multiple gradient echo. NMR IN BIOMEDICINE 2020; 33:e4272. [PMID: 32043682 DOI: 10.1002/nbm.4272] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
This study aimed to develop and test a simultaneous acquisition and analysis pipeline for voxel-based magnetic susceptibility and morphometry (VBMSM) on a single dataset using young volunteers, elderly healthy volunteers, and an Alzheimer's disease (AD) group. 3D T1 -weighted and multi-echo phase images for VBM and quantitative susceptibility mapping (QSM) were simultaneously acquired using a magnetization-prepared spoiled turbo multiple gradient echo sequence with inversion pulse for QSM (MP-QSM). The magnitude image was split into gray matter (GM) and white matter (WM) and was spatially normalized. The susceptibility map was reconstructed from the phase images. The segmented image and susceptibility map were compared with those obtained from conventional multiple spoiled gradient echo (mGRE) and MP-spoiled gradient echo (MP-GRE) in healthy volunteers to validate the availability of MP-QSM by numerical measurements. To assess the feasibility of the VBMSM analysis pipeline, voxel-based comparisons of susceptibility and morphometry in MP-QSM were conducted in volunteers with a bimodal age distribution, and in elderly volunteers and the AD group, using spatially normalized GM and WM volume images and a susceptibility map. GM/WM contrasts in MP-QSM, MP-GRE, and mGRE were 0.14 ± 0.011, 0.17 ± 0.015, and 0.045 ± 0.010, respectively. Segmented GM and WM volumes in the MP-QSM closely coincided with those in the MP-GRE. Region of interest analyses indicated that the mean susceptibility values in MP-QSM were completely in agreement with those in mGRE. In an evaluation of the aging effect, a significant increase and decrease in susceptibility and volume were found by VBMSM in deep GM and WM, respectively. Between the elderly volunteers and the AD group, the characteristic susceptibility and volume changes in GM and WM were observed. The proposed MP-QSM sequence makes it possible to acquire acceptable-quality images for simultaneous analysis and determine brain atrophy and susceptibility distribution without image registration by using voxel-based analyses.
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Affiliation(s)
- Hirohito Kan
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
| | - Yuto Uchida
- Department of Neurology, Nagoya City University, Nagoya City, Aichi, Japan
- Department of Neurology, Toyokawa City Hospital, Toyokawa, Aichi, Japan
| | - Nobuyuki Arai
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
| | - Yoshino Ueki
- Department of Rehabilitation Medicine, Nagoya City University, Nagoya City, Aichi, Japan
| | - Toshitaka Aoki
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
| | - Harumasa Kasai
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
| | - Hiroshi Kunitomo
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
| | - Yasujiro Hirose
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
| | - Noriyuki Matsukawa
- Department of Neurology, Nagoya City University, Nagoya City, Aichi, Japan
| | - Yuta Shibamoto
- Department of Radiology, Nagoya City University Hospital, Nagoya City, Aichi, Japan
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92
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Fan AP, Khalil AA, Fiebach JB, Zaharchuk G, Villringer A, Villringer K, Gauthier CJ. Elevated brain oxygen extraction fraction measured by MRI susceptibility relates to perfusion status in acute ischemic stroke. J Cereb Blood Flow Metab 2020; 40:539-551. [PMID: 30732551 PMCID: PMC7026852 DOI: 10.1177/0271678x19827944] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent clinical trials of new revascularization therapies in acute ischemic stroke have highlighted the importance of physiological imaging to identify optimal treatments for patients. Oxygen extraction fraction (OEF) is a hallmark of at-risk tissue in stroke, and can be quantified from the susceptibility effect of deoxyhemoglobin molecules in venous blood on MRI phase scans. We measured OEF within cerebral veins using advanced quantitative susceptibility mapping (QSM) MRI reconstructions in 20 acute stroke patients. Absolute OEF was elevated in the affected (29.3 ± 3.4%) versus the contralateral hemisphere (25.5 ± 3.1%) of patients with large diffusion-perfusion lesion mismatch (P = 0.032). In these patients, OEF negatively correlated with relative CBF measured by dynamic susceptibility contrast MRI (P = 0.004), suggesting compensation for reduced flow. Patients with perfusion-diffusion match or no hypo-perfusion showed less OEF difference between hemispheres. Nine patients received longitudinal assessment and showed OEF ratio (affected to contralateral) of 1.2 ± 0.1 at baseline that normalized (decreased) to 1.0 ± 0.1 at follow-up three days later (P = 0.03). Our feasibility study demonstrates that QSM MRI can non-invasively quantify OEF in stroke patients, relates to perfusion status, and is sensitive to OEF changes over time. Clinical trial registration: Longitudinal MRI examinations of patients with brain ischemia and blood brain barrier permeability; clinicaltrials.org :NCT02077582.
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Affiliation(s)
- Audrey P Fan
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Ahmed A Khalil
- Center for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,Berlin School of Mind and Brain, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Jochen B Fiebach
- Center for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Greg Zaharchuk
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Arno Villringer
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.,Berlin School of Mind and Brain, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kersten Villringer
- Center for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Claudine J Gauthier
- Department of Physics, Concordia University, Montreal, Canada.,Montreal Heart Institute, Montreal, Canada
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93
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Jorge J, Gretsch F, Najdenovska E, Tuleasca C, Levivier M, Maeder P, Gallichan D, Marques JP, Bach Cuadra M. Improved susceptibility-weighted imaging for high contrast and resolution thalamic nuclei mapping at 7T. Magn Reson Med 2020; 84:1218-1234. [PMID: 32052486 DOI: 10.1002/mrm.28197] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE The thalamus is an important brain structure and neurosurgical target, but its constituting nuclei are challenging to image non-invasively. Recently, susceptibility-weighted imaging (SWI) at ultra-high field has shown promising capabilities for thalamic nuclei mapping. In this work, several methodological improvements were explored to enhance SWI quality and contrast, and specifically its ability for thalamic imaging. METHODS High-resolution SWI was performed at 7T in healthy participants, and the following techniques were applied: (a) monitoring and retrospective correction of head motion and B0 perturbations using integrated MR navigators, (b) segmentation and removal of venous vessels on the SWI data using vessel enhancement filtering, and (c) contrast enhancement by tuning the parameters of the SWI phase-magnitude combination. The resulting improvements were evaluated with quantitative metrics of image quality, and by comparison to anatomo-histological thalamic atlases. RESULTS Even with sub-millimeter motion and natural breathing, motion and field correction produced clear improvements in both magnitude and phase data quality (76% and 41%, respectively). The improvements were stronger in cases of larger motion/field deviations, mitigating the dependence of image quality on subject performance. Optimizing the SWI phase-magnitude combination yielded substantial improvements in image contrast, particularly in the thalamus, well beyond previously reported SWI results. The atlas comparisons provided compelling evidence of anatomical correspondence between SWI features and several thalamic nuclei, for example, the ventral intermediate nucleus. Vein detection performed favorably inside the thalamus, and vein removal further improved visualization. CONCLUSION Altogether, the proposed developments substantially improve high-resolution SWI, particularly for thalamic nuclei imaging.
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Affiliation(s)
- João Jorge
- Medical Image Analysis Laboratory, Center for Biomedical Imaging (CIBM), University of Lausanne, Lausanne, Switzerland.,Laboratory for Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Frédéric Gretsch
- Laboratory for Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elena Najdenovska
- Medical Image Analysis Laboratory, Center for Biomedical Imaging (CIBM), University of Lausanne, Lausanne, Switzerland.,Department of Radiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Constantin Tuleasca
- Department of Clinical Neurosciences, Neurosurgery Service and Gamma Knife Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.,Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Marc Levivier
- Department of Clinical Neurosciences, Neurosurgery Service and Gamma Knife Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.,Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Philippe Maeder
- Department of Radiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Daniel Gallichan
- Cardiff University Brain Research Imaging Centre, School of Engineering, Cardiff University, Cardiff, UK
| | - José P Marques
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Meritxell Bach Cuadra
- Medical Image Analysis Laboratory, Center for Biomedical Imaging (CIBM), University of Lausanne, Lausanne, Switzerland.,Department of Radiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland.,Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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94
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MRI T 2 and T 2* relaxometry to visualize neuromelanin in the dorsal substantia nigra pars compacta. Neuroimage 2020; 211:116625. [PMID: 32058001 DOI: 10.1016/j.neuroimage.2020.116625] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/19/2022] Open
Abstract
Visualizing gradual changes in neuromelanin distribution within the substantia nigra is an important metric used to monitor the progression of Parkinsonism. This study aimed to identify the origin of the mismatch region between magnetic resonance transverse relaxation times (T2 and T2*) in the substantia nigra and investigate its feasibility and implications for in vivo detection of neuromelanin as a clinical biomarker. The relationships between neuromelanin distribution assessed by histological staining and the area of T2 and T2* mismatch determined by high- and low-resolution magnetic resonance relaxometry at 7T were directly compared in two normal and one depigmented substantia nigra collected at postmortem. In vivo feasibility of assessing T2 and T2* mismatch, clinically, was investigated using 3T magnetic resonance imaging. In the normal postmortem substantia nigra tissue, the T2 and T2* mismatch region exhibiting a linear pattern was strongly colocalized with neuromelanin distribution along the dorsal substantia nigra pars compacta, but a negligible amount of dorsal mismatch was observed in the depigmented brain. The regions of T2 and T2* mismatch from MRI, neuromelanin pigments from histology, and elevated iron signals from mass spectrometry were spatially overlapped for a normal postmortem brain. In preliminary in vivo studies, a similar, linear T2 and T2* mismatch region was observed in the dorsal area of the substantia nigra in eight normal subjects; this mismatch was significantly obscured in eight Parkinson's disease patients. The length of the dorsal linear mismatch line based on the T2*-T2 mask was significantly shorter in the Parkinson's disease patients compared to normal controls; this result was corroborated by reduced striatal uptake of [18F] FP-CIT dopamine transporters assessed by positron emission tomography scans. In conclusion, the measurement of T2 and T2* mismatch could serve as a complementary imaging biomarker to visualize the dorsal region of the substantia nigra pars compacta, which contains large amounts of neuromelanin.
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95
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Ruetten PPR, Cluroe AD, Usman A, Priest AN, Gillard JH, Graves MJ. Simultaneous MRI water‐fat separation and quantitative susceptibility mapping of carotid artery plaque pre‐ and post‐ultrasmall superparamagnetic iron oxide‐uptake. Magn Reson Med 2020; 84:686-697. [DOI: 10.1002/mrm.28151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/28/2019] [Accepted: 12/08/2019] [Indexed: 12/20/2022]
Affiliation(s)
| | - Alison D. Cluroe
- Department of Histopathology Addenbrooke’s Hospital Histopathology, Cambridge United Kingdom
| | - Ammara Usman
- Department of Radiology University of Cambridge Cambridge United Kingdom
| | - Andrew N. Priest
- Department of Medical Physics Cambridge University Hospitals NHS Foundation Trust Cambridge United Kingdom
| | | | - Martin J. Graves
- Department of Radiology Cambridge University Hospitals NHS Foundation Trust Cambridge United Kingdom
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96
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Vinayagamani S, Sheelakumari R, Sabarish S, Senthilvelan S, Ros R, Thomas B, Kesavadas C. Quantitative Susceptibility Mapping: Technical Considerations and Clinical Applications in Neuroimaging. J Magn Reson Imaging 2020; 53:23-37. [DOI: 10.1002/jmri.27058] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/28/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - R Sheelakumari
- Department of Imaging Sciences and Interventional Radiology Trivandrum India
| | - Sekar Sabarish
- Department of Imaging Sciences and Interventional Radiology Trivandrum India
| | | | - Roopa Ros
- Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology Trivandrum India
| | - Bejoy Thomas
- Department of Imaging Sciences and Interventional Radiology Trivandrum India
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97
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Liu Z, Wen Y, Spincemaille P, Zhang S, Yao Y, Nguyen T, Wang Y. Automated adaptive preconditioner for quantitative susceptibility mapping. Magn Reson Med 2020; 83:271-285. [PMID: 31402519 PMCID: PMC6778703 DOI: 10.1002/mrm.27900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
Abstract
PURPOSE To develop an automated adaptive preconditioner for QSM reconstruction with improved susceptibility quantification accuracy and increased image quality. THEORY AND METHODS The total field was used to rapidly produce an approximate susceptibility map, which was then averaged and trended over R 2 ∗ binning to generate a spatially varying distribution of preconditioning values. This automated adaptive preconditioner was used to reconstruct QSM via total field inversion and was compared with its empirical counterparts in a numerical simulation, a brain experiment with 5 healthy subjects and 5 patients with intracerebral hemorrhage, and a cardiac experiment with 3 healthy subjects. RESULTS Among evaluated preconditioners, the automated adaptive preconditioner achieved the fastest convergence in reducing the RMSE of the QSM in the simulation, suppressed hemorrhage-associated artifacts while preserving surrounding brain tissue contrasts, and provided cardiac chamber oxygenation values consistent with those reported in the literature. CONCLUSION An automated adaptive preconditioner allows high-quality QSM from the total field in imaging various anatomies with dynamic susceptibility ranges.
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Affiliation(s)
- Zhe Liu
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Yan Wen
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Pascal Spincemaille
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Shun Zhang
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
- Department of Radiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yihao Yao
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
- Department of Radiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Thanh Nguyen
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Yi Wang
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
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98
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Multi-site harmonization of 7 tesla MRI neuroimaging protocols. Neuroimage 2019; 206:116335. [PMID: 31712167 PMCID: PMC7212005 DOI: 10.1016/j.neuroimage.2019.116335] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022] Open
Abstract
Increasing numbers of 7 T (7 T) magnetic resonance imaging (MRI) scanners are in research and clinical use. 7 T MRI can increase the scanning speed, spatial resolution and contrast-to-noise-ratio of many neuroimaging protocols, but technical challenges in implementation have been addressed in a variety of ways across sites. In order to facilitate multi-centre studies and ensure consistency of findings across sites, it is desirable that 7 T MRI sites implement common high-quality neuroimaging protocols that can accommodate different scanner models and software versions. With the installation of several new 7 T MRI scanners in the United Kingdom, the UK7T Network was established with an aim to create a set of harmonized structural and functional neuroimaging sequences and protocols. The Network currently includes five sites, which use three different scanner platforms, provided by two different vendors. Here we describe the harmonization of functional and anatomical imaging protocols across the three different scanner models, detailing the necessary changes to pulse sequences and reconstruction methods. The harmonized sequences are fully described, along with implementation details. Example datasets acquired from the same subject on all Network scanners are made available. Based on these data, an evaluation of the harmonization is provided. In addition, the implementation and validation of a common system calibration process is described.
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99
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Guo Y, Liu Z, Wen Y, Spincemaille P, Zhang H, Jafari R, Zhang S, Eskreis-Winkler S, Gillen KM, Yi P, Feng Q, Feng Y, Wang Y. Quantitative susceptibility mapping of the spine using in-phase echoes to initialize inhomogeneous field and R2* for the nonconvex optimization problem of fat-water separation. NMR IN BIOMEDICINE 2019; 32:e4156. [PMID: 31424131 DOI: 10.1002/nbm.4156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
Quantitative susceptibility mapping (QSM) of human spinal vertebrae from a multi-echo gradient-echo (GRE) sequence is challenging, because comparable amounts of fat and water in the vertebrae make it difficult to solve the nonconvex optimization problem of fat-water separation (R2*-IDEAL) for estimating the magnetic field induced by tissue susceptibility. We present an in-phase (IP) echo initialization of R2*-IDEAL for QSM in the spinal vertebrae. Ten healthy human subjects were recruited for spine MRI. A 3D multi-echo GRE sequence was implemented to acquire out-phase and IP echoes. For the IP method, the R2* and field maps estimated by separately fitting the magnitude and phase of IP echoes were used to initialize gradient search R2*-IDEAL to obtain final R2*, field, water, and fat maps, and the final field map was used to generate QSM. The IP method was compared with the existing Zero method (initializing the field to zero), VARPRO-GC (variable projection using graphcuts but still initializing the field to zero), and SPURS (simultaneous phase unwrapping and removal of chemical shift using graphcuts for initialization) on both simulation and in vivo data. The single peak fat model was also compared with the multi-peak fat model. There was no substantial difference on QSM between the single peak and multi-peak fat models, but there were marked differences among different initialization methods. The simulations demonstrated that IP provided the lowest error in the field map. Compared to Zero, VARPRO-GC and SPURS, the proposed IP method provided substantially improved spine QSM in all 10 subjects.
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Affiliation(s)
- Yihao Guo
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
- Department of Biomedical Engineering, Cornell University, Ithaca, New York
- Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, China
| | - Zhe Liu
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
- Department of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Yan Wen
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
- Department of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Pascal Spincemaille
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
| | - Honglei Zhang
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
| | - Ramin Jafari
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
- Department of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Shun Zhang
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
| | - Sarah Eskreis-Winkler
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
| | - Kelly M Gillen
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
| | - Peiwei Yi
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Qianjin Feng
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, China
| | - Yanqiu Feng
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou, China
| | - Yi Wang
- Department of Radiology, Weill Medical College of Cornell University, New York, New York
- Department of Biomedical Engineering, Cornell University, Ithaca, New York
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100
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Dhulipala PV, Shi C, Xie G, Wang H, Ji JX. MARBLES - Metal Artifact Based Landmark Enhanced Susceptibility Weighted Imaging For Interventional Device Localization In MRI. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:2611-2614. [PMID: 30440943 DOI: 10.1109/embc.2018.8512739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Susceptibility Weighted Imaging (SWI) is a method extensively studied for its application to improve contrast in MR imaging modality. The method enhances the visualization of magnetically susceptible content such as iron, calcium and zinc in the tissues by using the susceptibility differences in tissues to generate a unique image contrast. In this study, we propose an SWI based approach to improve the visualization of interventional devices in MRI data. Results obtained from two datasets (biopsy needle and brachytherapy seeds), indicate SWI to be suitable for visualization of the interventional devices, while also being computationally faster when compared with quantitative susceptibility mapping (QSM).
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