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Radunsky D, Solomon C, Stern N, Blumenfeld-Katzir T, Filo S, Mezer A, Karsa A, Shmueli K, Soustelle L, Duhamel G, Girard OM, Kepler G, Shrot S, Hoffmann C, Ben-Eliezer N. A comprehensive protocol for quantitative magnetic resonance imaging of the brain at 3 Tesla. PLoS One 2024; 19:e0297244. [PMID: 38820354 PMCID: PMC11142522 DOI: 10.1371/journal.pone.0297244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 01/01/2024] [Indexed: 06/02/2024] Open
Abstract
Quantitative MRI (qMRI) has been shown to be clinically useful for numerous applications in the brain and body. The development of rapid, accurate, and reproducible qMRI techniques offers access to new multiparametric data, which can provide a comprehensive view of tissue pathology. This work introduces a multiparametric qMRI protocol along with full postprocessing pipelines, optimized for brain imaging at 3 Tesla and using state-of-the-art qMRI tools. The total scan time is under 50 minutes and includes eight pulse-sequences, which produce range of quantitative maps including T1, T2, and T2* relaxation times, magnetic susceptibility, water and macromolecular tissue fractions, mean diffusivity and fractional anisotropy, magnetization transfer ratio (MTR), and inhomogeneous MTR. Practical tips and limitations of using the protocol are also provided and discussed. Application of the protocol is presented on a cohort of 28 healthy volunteers and 12 brain regions-of-interest (ROIs). Quantitative values agreed with previously reported values. Statistical analysis revealed low variability of qMRI parameters across subjects, which, compared to intra-ROI variability, was x4.1 ± 0.9 times higher on average. Significant and positive linear relationship was found between right and left hemispheres' values for all parameters and ROIs with Pearson correlation coefficients of r>0.89 (P<0.001), and mean slope of 0.95 ± 0.04. Finally, scan-rescan stability demonstrated high reproducibility of the measured parameters across ROIs and volunteers, with close-to-zero mean difference and without correlation between the mean and difference values (across map types, mean P value was 0.48 ± 0.27). The entire quantitative data and postprocessing scripts described in the manuscript are publicly available under dedicated GitHub and Figshare repositories. The quantitative maps produced by the presented protocol can promote longitudinal and multi-center studies, and improve the biological interpretability of qMRI by integrating multiple metrics that can reveal information, which is not apparent when examined using only a single contrast mechanism.
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Affiliation(s)
- Dvir Radunsky
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | - Chen Solomon
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | - Neta Stern
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | | | - Shir Filo
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aviv Mezer
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anita Karsa
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | | | | | | | - Gal Kepler
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Shai Shrot
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Ramat-Gan, Israel
| | - Chen Hoffmann
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Ramat-Gan, Israel
| | - Noam Ben-Eliezer
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Center for Advanced Imaging Innovation and Research (CAI2R), New-York University Langone Medical Center, New York, NY, United States of America
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Variability by region and method in human brain sodium concentrations estimated by 23Na magnetic resonance imaging: a meta-analysis. Sci Rep 2023; 13:3222. [PMID: 36828873 PMCID: PMC9957999 DOI: 10.1038/s41598-023-30363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Sodium imaging (23Na-MRI) is of interest in neurological conditions given potential sensitivity to the physiological and metabolic status of tissues. Benchmarks have so far been restricted to parenchyma or grey/white matter (GM/WM). We investigate (1) the availability of evidence, (2) regional pooled estimates and (3) variability attributable to region/methodology. MEDLINE literature search for tissue sodium concentration (TSC) measured in specified 'healthy' brain regions returned 127 reports, plus 278 retrieved from bibliographies. 28 studies met inclusion criteria, including 400 individuals. Reporting variability led to nested data structure, so we used multilevel meta-analysis and a random effects model to pool effect sizes. The pooled mean from 141 TSC estimates was 40.51 mM (95% CI 37.59-43.44; p < 0.001, I2Total=99.4%). Tissue as a moderator was significant (F214 = 65.34, p-val < .01). Six sub-regional pooled means with requisite statistical power were derived. We were unable to consider most methodological and demographic factors sought because of non-reporting, but each factor included beyond tissue improved model fit. Significant residual heterogeneity remained. The current estimates provide an empirical point of departure for better understanding in 23Na-MRI. Improving on current estimates supports: (1) larger, more representative data collection/sharing, including (2) regional data, and (3) agreement on full reporting standards.
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Yao J, Morrison MA, Jakary A, Avadiappan S, Chen Y, Luitjens J, Glueck J, Driscoll T, Geschwind MD, Nelson AB, Villanueva-Meyer JE, Hess CP, Lupo JM. Comparison of quantitative susceptibility mapping methods for iron-sensitive susceptibility imaging at 7T: An evaluation in healthy subjects and patients with Huntington's disease. Neuroimage 2023; 265:119788. [PMID: 36476567 DOI: 10.1016/j.neuroimage.2022.119788] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/08/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Quantitative susceptibility mapping (QSM) is a promising tool for investigating iron dysregulation in neurodegenerative diseases, including Huntington's disease (HD). Many diverse methods have been proposed to generate accurate and robust QSM images. In this study, we evaluated the performance of different dipole inversion algorithms for iron-sensitive susceptibility imaging at 7T on healthy subjects of a large age range and patients with HD. We compared an iterative least-squares-based method (iLSQR), iterative methods that use regularization, single-step approaches, and deep learning-based techniques. Their performance was evaluated by comparing: (1) deviations from a multiple-orientation QSM reference; (2) visual appearance of QSM maps and the presence of artifacts; (3) susceptibility in subcortical brain regions with age; (4) regional brain susceptibility with published postmortem brain iron quantification; and (5) susceptibility in HD-affected basal ganglia regions between HD subjects and healthy controls. We found that single-step QSM methods with either total variation or total generalized variation constraints (SSTV/SSTGV) and the single-step deep learning method iQSM generally provided the best performance in terms of correlation with iron deposition and were better at differentiating between healthy controls and premanifest HD individuals, while deep learning QSM methods trained with multiple-orientation susceptibility data created QSM maps that were most similar to the multiple orientation reference and with the best visual scores.
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Affiliation(s)
- Jingwen Yao
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA
| | - Melanie A Morrison
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA
| | - Angela Jakary
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA
| | - Sivakami Avadiappan
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA
| | - Yicheng Chen
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA; UCSF/UC Berkeley Graduate Program in Bioengineering, San Francisco & Berkeley, CA, USA; Meta Platforms, Inc., Mountain View, CA, USA
| | - Johanna Luitjens
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA; Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Julia Glueck
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Theresa Driscoll
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Michael D Geschwind
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Alexandra B Nelson
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | | | - Christopher P Hess
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Janine M Lupo
- Department of Radiology and Biomedical Imaging, UCSF, San Francisco, CA, USA; UCSF/UC Berkeley Graduate Program in Bioengineering, San Francisco & Berkeley, CA, USA.
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Berman S, Drori E, Mezer AA. Spatial profiles provide sensitive MRI measures of the midbrain micro- and macrostructure. Neuroimage 2022; 264:119660. [PMID: 36220534 DOI: 10.1016/j.neuroimage.2022.119660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/15/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022] Open
Abstract
The midbrain is the rostral-most part of the brainstem. It contains numerous nuclei and white matter tracts, which are involved in motor, auditory and visual processing, and changes in their structure and function have been associated with aging, as well as neurodegenerative disorders. Current tools for estimating midbrain subregions and their structure with MRI require high resolution and multi-parametric quantitative MRI measures. We propose an approach that relies on morphology to calculate profiles along the midbrain and show these profiles are sensitive to the underlying macrostructure of the midbrain. First, we show that the midbrain structure can be sampled, within subject space, along three main axes of the left and right midbrain, producing profiles that are similar across subjects. We use two data sets with different field strengths, that contain R1, R2* and QSM maps and show that the profiles are highly correlated both across subjects and between datasets. Next, we compare profiles of the midbrain that sample ROIs, and show that the profiles along the first two axes sample the midbrain in a way that reliably separates the main structures, i.e., the substantia nigra, the red nucleus, and periaqueductal gray. We further show that age differences which are localized to specific nuclei, are reflected in the profiles. Finally, we generalize the same approach to calculate midbrain profiles on a third clinically relevant dataset using HCP subjects, with metrics such as the diffusion tensor and semi-quantitative data such as T1w/T2w maps. Our results suggest that midbrain profiles, both of quantitative and semi-quantitative estimates are sensitive to the underlying macrostructure of the midbrain. The midbrain profiles are calculated in native space, and rely on simple measurements. We show that it is robust and can be easily expanded to different datasets, and as such we hope that it will be of great use to the community and to the study of the midbrain in particular.
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Affiliation(s)
- Shai Berman
- The Edmond and Lily Safra Center for Brain Science, the Hebrew University of Jerusalem, Israel; Mortimer B. Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY, United States.
| | - Elior Drori
- The Edmond and Lily Safra Center for Brain Science, the Hebrew University of Jerusalem, Israel
| | - Aviv A Mezer
- The Edmond and Lily Safra Center for Brain Science, the Hebrew University of Jerusalem, Israel
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