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Autio JA, Uematsu A, Ikeda T, Ose T, Hou Y, Magrou L, Kimura I, Ohno M, Murata K, Coalson T, Kennedy H, Glasser MF, Van Essen DC, Hayashi T. Charting Cortical-Layer Specific Area Boundaries Using Gibbs' Ringing Attenuated T1w/T2w-FLAIR Myelin MRI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.27.615294. [PMID: 39386722 PMCID: PMC11463467 DOI: 10.1101/2024.09.27.615294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Cortical areas have traditionally been defined by their distinctive layer cyto- and/or myelo- architecture using postmortem histology. Recent studies have delineated many areas by measuring overall cortical myelin content and its spatial gradients using the T1w/T2w ratio MRI in living primates, including humans. While T1w/T2w studies of areal transitions might benefit from using the layer profile of this myelin-related contrast, a significant confound is Gibbs' ringing artefact, which produces signal fluctuations resembling cortical layers. Here, we address these issues with a novel approach using cortical layer thickness-adjusted T1w/T2w-FLAIR imaging, which effectively cancels out Gibbs' ringing artefacts while enhancing intra- cortical myelin contrast. Whole-brain MRI measures were mapped onto twelve equivolumetric layers, and layer-specific sharp myeloarchitectonic transitions were identified using spatial gradients resulting in a putative 182 area/subarea partition of the macaque cerebral cortex. The myelin maps exhibit unexpectedly high homology with humans suggesting cortical myelin shares the same developmental program across the species. Comparison with histological Gallyas myelin stains explains over 80% of the variance in the laminar T1w/T2w-FLAIR profiles, substantiating the validity of the method. Altogether, our approach provides a novel, noninvasive means for precision mapping layer myeloarchitecture in the primate cerebral cortex, advancing the pioneering work of classical neuroanatomists.
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Lee CY, Mani M. 2D CAIPI accelerated 3D multi-slab diffusion weighted EPI combined with qModeL reconstruction for fast high resolution microstructure imaging. Magn Reson Imaging 2024; 111:57-66. [PMID: 38599504 PMCID: PMC11179987 DOI: 10.1016/j.mri.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE To develop acceleration strategies for 3D multi-slab diffusion weighted imaging (3D ms-DWI) for enabling applications that require simultaneously high spatial (1 mm isotropic) and angular (> 30 directions) resolutions. METHODS 3D ms-DWI offers high SNR-efficiency, with the ability to achieve high isotropic spatial resolution, yet suffers from long scan-times for studies requiring high angular resolutions. We develop 6D k-q space acceleration strategies to reduce the scan-time. Specifically, we develop non-uniform 3D ky-kz under-sampling employing a shot-selective 2D CAIPI sampling approach. To achieve inter-shot phase-compensation, 2D navigators were employed that utilize the same CAIPI trajectory. An iterative model-based 3D multi-shot reconstruction was designed by incorporating phase into the forward encoding process. Additionally, the shot-selective non-uniform ky-kz CAIPI acceleration was randomized along the q-dimension. The 3D model-based multi-shot reconstruction is then extended to a joint reconstruction that simultaneously reconstructs all the q-space points, with the help of a spatial total variation and deep-learned q-space regularization. RESULTS The proposed reconstruction is shown to achieve adequate phase-compensation in both 2D CAIPI accelerated and additional ky-kz under-sampled cases. Using retrospective under-sampling experiments, we show that k-q accelerations close a factor of 12 can be achieved with a reconstruction error < 3% for both single and multi-shell data. This translates to a scan-time reduction by 3-fold for experiments with simultaneously high spatial and angular resolutions. CONCLUSION The proposed method facilitates the utilization of 3D ms-DWI for simultaneously high k-q resolution applications with close to 3× reduced scan-time.
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Affiliation(s)
- Chu-Yu Lee
- Department of Radiology, University of Iowa, Iowa City, IA, United States of America
| | - Merry Mani
- Department of Radiology, University of Iowa, Iowa City, IA, United States of America.
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3
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Chen X, Wu W, Chiew M. Motion compensated structured low-rank reconstruction for 3D multi-shot EPI. Magn Reson Med 2024; 91:2443-2458. [PMID: 38361309 DOI: 10.1002/mrm.30019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/08/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
PURPOSE The 3D multi-shot EPI imaging offers several benefits including higher SNR and high isotropic resolution compared to 2D single shot EPI. However, it suffers from shot-to-shot inconsistencies arising from physiologically induced phase variations and bulk motion. This work proposed a motion compensated structured low-rank (mcSLR) reconstruction method to address both issues for 3D multi-shot EPI. METHODS Structured low-rank reconstruction has been successfully used in previous work to deal with inter-shot phase variations for 3D multi-shot EPI imaging. It circumvents the estimation of phase variations by reconstructing an individual image for each phase state which are then sum-of-squares combined, exploiting their linear interdependency encoded in structured low-rank constraints. However, structured low-rank constraints become less effective in the presence of inter-shot motion, which corrupts image magnitude consistency and invalidates the linear relationship between shots. Thus, this work jointly models inter-shot phase variations and motion corruptions by incorporating rigid motion compensation for structured low-rank reconstruction, where motion estimates are obtained in a fully data-driven way without relying on external hardware or imaging navigators. RESULTS Simulation and in vivo experiments at 7T have demonstrated that the mcSLR method can effectively reduce image artifacts and improve the robustness of 3D multi-shot EPI, outperforming existing methods which only address inter-shot phase variations or motion, but not both. CONCLUSION The proposed mcSLR reconstruction compensates for rigid motion, and thus improves the validity of structured low-rank constraints, resulting in improved robustness of 3D multi-shot EPI to both inter-shot motion and phase variations.
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Affiliation(s)
- Xi Chen
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Wenchuan Wu
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Chiew
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, Oxfordshire, UK
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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4
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Wu CY, Jin J, Dixon C, Maillet D, Barth M, Cloos MA. Velocity selective spin labeling using parallel transmission. Magn Reson Med 2024; 91:1576-1585. [PMID: 38044841 DOI: 10.1002/mrm.29955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/29/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
PURPOSE Ultra-high field (UHF) provides improved SNR which greatly benefits SNR starved imaging techniques such as perfusion imaging. However, transmit field (B1 + ) inhomogeneities commonly observed at UHF hinders the excitation uniformity. Here we show how replacing standard excitation pulses with parallel transmit pulses can improve efficiency of velocity selective labeling. METHODS The standard tip-down and tip-up excitation pulses found in a velocity selective preparation module were replaced with tailored non-selective kT -points pulse solutions. Bloch simulations and experimental validation on a custom-built flow phantom and in vivo was performed to evaluate different pulse configurations in circularly polarized mode (CP-mode) and parallel transmit (pTx) mode. RESULTS Tailored pTx pulses significantly improved velocity selective labeling fidelity and signal uniformity. The transverse magnetization normalized RMS error was reduced from 0.489 to 0.047 when compared to standard rectangular pulses played in CP-mode. Simulations showed that manipulation of time symmetry in the tailored pTx pulses is vital in minimizing residual magnetization. In addition, in vivo experiments achieved a 44% lower RF power output and a shorter pulse duration when compared to using adiabatic pulses in CP-mode. CONCLUSION Using tailored pTx pulses for excitation within a velocity selective labeling preparation mitigated transmit field artifacts and improved SNR and contrast fidelity. The improvement in labeling efficiency highlights the potential of using pTx to improve robustness and accessibility of flow-based sequences such as velocity selective spin labeling at ultra-high field.
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Affiliation(s)
- Chia-Yin Wu
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, Australia
- ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, Queensland, Australia
- School of Electrical Engineering and Computer Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Jin Jin
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, Australia
- ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, Queensland, Australia
- School of Electrical Engineering and Computer Science, The University of Queensland, St Lucia, Queensland, Australia
- Siemens Healthcare Pty Ltd, Brisbane, Queensland, Australia
| | - Carl Dixon
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, Australia
| | - Donald Maillet
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, Australia
| | - Markus Barth
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, Australia
- ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, Queensland, Australia
- School of Electrical Engineering and Computer Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Martijn A Cloos
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, Australia
- ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, Queensland, Australia
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5
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Foster SL, Breukelaar IA, Ekanayake K, Lewis S, Korgaonkar MS. Functional Magnetic Resonance Imaging of the Amygdala and Subregions at 3 Tesla: A Scoping Review. J Magn Reson Imaging 2024; 59:361-375. [PMID: 37352130 DOI: 10.1002/jmri.28836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/25/2023] Open
Abstract
The amygdalae are a pair of small brain structures, each of which is composed of three main subregions and whose function is implicated in neuropsychiatric conditions. Functional Magnetic Resonance Imaging (fMRI) has been utilized extensively in investigation of amygdala activation and functional connectivity (FC) with most clinical research sites now utilizing 3 Tesla (3T) MR systems. However, accurate imaging and analysis remains challenging not just due to the small size of the amygdala, but also its location deep in the temporal lobe. Selection of imaging parameters can significantly impact data quality with implications for the accuracy of study results and validity of conclusions. Wide variation exists in acquisition protocols with spatial resolution of some protocols suboptimal for accurate assessment of the amygdala as a whole, and for measuring activation and FC of the three main subregions, each of which contains multiple nuclei with specialized roles. The primary objective of this scoping review is to provide a broad overview of 3T fMRI protocols in use to image the activation and FC of the amygdala with particular reference to spatial resolution. The secondary objective is to provide context for a discussion culminating in recommendations for a standardized protocol for imaging activation of the amygdala and its subregions. As the advantages of big data and protocol harmonization in imaging become more apparent so, too, do the disadvantages of data heterogeneity. EVIDENCE LEVEL: 3 TECHNICAL EFFICACY: Stage 2.
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Affiliation(s)
- Sheryl L Foster
- Sydney School of Health Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Radiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Isabella A Breukelaar
- Brain Dynamics Centre, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Kanchana Ekanayake
- University Library, The University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Lewis
- Sydney School of Health Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Mayuresh S Korgaonkar
- Brain Dynamics Centre, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
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Pollak C, Kügler D, Breteler MMB, Reuter M. Quantifying MR Head Motion in the Rhineland Study - A Robust Method for Population Cohorts. Neuroimage 2023; 275:120176. [PMID: 37209757 DOI: 10.1016/j.neuroimage.2023.120176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/22/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Head motion during MR acquisition reduces image quality and has been shown to bias neuromorphometric analysis. The quantification of head motion, therefore, has both neuroscientific as well as clinical applications, for example, to control for motion in statistical analyses of brain morphology, or as a variable of interest in neurological studies. The accuracy of markerless optical head tracking, however, is largely unexplored. Furthermore, no quantitative analysis of head motion in a general, mostly healthy population cohort exists thus far. In this work, we present a robust registration method for the alignment of depth camera data that sensitively estimates even small head movements of compliant participants. Our method outperforms the vendor-supplied method in three validation experiments: 1. similarity to fMRI motion traces as a low-frequency reference, 2. recovery of the independently acquired breathing signal as a high-frequency reference, and 3. correlation with image-based quality metrics in structural T1-weighted MRI. In addition to the core algorithm, we establish an analysis pipeline that computes average motion scores per time interval or per sequence for inclusion in downstream analyses. We apply the pipeline in the Rhineland Study, a large population cohort study, where we replicate age and body mass index (BMI) as motion correlates and show that head motion significantly increases over the duration of the scan session. We observe weak, yet significant interactions between this within-session increase and age, BMI, and sex. High correlations between fMRI and camera-based motion scores of proceeding sequences further suggest that fMRI motion estimates can be used as a surrogate score in the absence of better measures to control for motion in statistical analyses.
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Affiliation(s)
- Clemens Pollak
- AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Kügler
- AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Martin Reuter
- AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA.
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7
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Claus J, Upadhyay N, Maurer A, Klein J, Scheef L, Daamen M, Martin JA, Stirnberg R, Radbruch A, Attenberger U, Stöcker T, Boecker H. Physical Activity Alters Functional Connectivity of Orbitofrontal Cortex Subdivisions in Healthy Young Adults: A Longitudinal fMRI Study. Healthcare (Basel) 2023; 11:healthcare11050689. [PMID: 36900693 PMCID: PMC10001322 DOI: 10.3390/healthcare11050689] [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: 12/23/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Physical activity (PA) plays an important role in affect processing. Studies describe the orbitofrontal cortex (OFC) as a major hub for emotion processing and the pathophysiology of affective disorders. Subregions of the OFC show diverse functional connectivity (FC) topographies, but the effect of chronic PA on subregional OFC FC still lacks scientific understanding. Therefore, we aimed at investigating the effects of regular PA on the FC topographies of OFC subregions in healthy individuals within a longitudinal randomized controlled exercise study. Participants (age: 18-35 years) were randomly assigned to either an intervention group (IG; N = 18) or a control group (CG; N = 10). Fitness assessments, mood questionnaires, and resting state functional magnetic resonance imaging (rsfMRI) were performed four times over the duration of 6 months. Using a detailed parcellation of the OFC, we created subregional FC topography maps at each time point and applied a linear mixed model to assess the effects of regular PA. The posterior-lateral right OFC showed a group and time interaction, revealing decreased FC with the left dorsolateral prefrontal cortex in the IG, while FC in the CG increased. Group and time interaction in the anterior-lateral right OFC with the right middle frontal gyrus was driven by increased FC in the IG. The posterior-lateral left OFC showed a group and time interaction based on differential change in FC to the left postcentral gyrus and the right occipital gyrus. This study emphasized regionally distinctive FC changes induced by PA within the lateral OFC territory, while providing aspects for further research.
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Affiliation(s)
- Jannik Claus
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Neeraj Upadhyay
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases, Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Angelika Maurer
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Julian Klein
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Lukas Scheef
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Marcel Daamen
- German Center for Neurodegenerative Diseases, Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Jason Anthony Martin
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Rüdiger Stirnberg
- German Center for Neurodegenerative Diseases, Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Alexander Radbruch
- German Center for Neurodegenerative Diseases, Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
- Department of Neuroradiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Ulrike Attenberger
- Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases, Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Henning Boecker
- Clinical Functional Imaging Lab, Department of Diagnostic and Interventional Radiology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases, Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
- Correspondence:
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8
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Faes LK, De Martino F, Huber L(R. Cerebral blood volume sensitive layer-fMRI in the human auditory cortex at 7T: Challenges and capabilities. PLoS One 2023; 18:e0280855. [PMID: 36758009 PMCID: PMC9910709 DOI: 10.1371/journal.pone.0280855] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/09/2023] [Indexed: 02/10/2023] Open
Abstract
The development of ultra high field fMRI signal readout strategies and contrasts has led to the possibility of imaging the human brain in vivo and non-invasively at increasingly higher spatial resolutions of cortical layers and columns. One emergent layer-fMRI acquisition method with increasing popularity is the cerebral blood volume sensitive sequence named vascular space occupancy (VASO). This approach has been shown to be mostly sensitive to locally-specific changes of laminar microvasculature, without unwanted biases of trans-laminar draining veins. Until now, however, VASO has not been applied in the technically challenging cortical area of the auditory cortex. Here, we describe the main challenges we encountered when developing a VASO protocol for auditory neuroscientific applications and the solutions we have adopted. With the resulting protocol, we present preliminary results of laminar responses to sounds and as a proof of concept for future investigations, we map the topographic representation of frequency preference (tonotopy) in the auditory cortex.
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Affiliation(s)
- Lonike K. Faes
- Faculty of Psychology and Neuroscience, Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands
- * E-mail:
| | - Federico De Martino
- Faculty of Psychology and Neuroscience, Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Laurentius (Renzo) Huber
- Faculty of Psychology and Neuroscience, Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands
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9
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Mesoscopic in vivo human T 2* dataset acquired using quantitative MRI at 7 Tesla. Neuroimage 2022; 264:119733. [PMID: 36375782 DOI: 10.1016/j.neuroimage.2022.119733] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/15/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
Mesoscopic (0.1-0.5 mm) interrogation of the living human brain is critical for advancing neuroscience and bridging the resolution gap with animal models. Despite the variety of MRI contrasts measured in recent years at the mesoscopic scale, in vivo quantitative imaging of T2* has not been performed. Here we provide a dataset containing empirical T2* measurements acquired at 0.35 × 0.35 × 0.35 mm3 voxel resolution using 7 Tesla MRI. To demonstrate unique features and high quality of this dataset, we generate flat map visualizations that reveal fine-scale cortical substructures such as layers and vessels, and we report quantitative depth-dependent T2* (as well as R2*) values in primary visual cortex and auditory cortex that are highly consistent across subjects. This dataset is freely available at https://doi.org/10.17605/OSF.IO/N5BJ7, and may prove useful for anatomical investigations of the human brain, as well as for improving our understanding of the basis of the T2*-weighted (f)MRI signal.
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10
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Effects of a 6-Month Aerobic Exercise Intervention on Mood and Amygdala Functional Plasticity in Young Untrained Subjects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19106078. [PMID: 35627616 PMCID: PMC9140773 DOI: 10.3390/ijerph19106078] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 12/04/2022]
Abstract
Acute exercise has beneficial effects on mood and is known to induce modulations in functional connectivity (FC) within the emotional network. However, the long-term effects of exercise on affective brain circuits remain largely unknown. Here, we investigated the effects of 6 months of regular exercise on mood, amygdala structure, and functional connectivity. This study comprised N = 18 healthy sedentary subjects assigned to an intervention group (IG; 23.9 ± 3.9 years; 3 trainings/week) and N = 10 subjects assigned to a passive control group (CG; 23.7 ± 4.2 years). At baseline and every two months, performance diagnostics, mood questionnaires, and structural and resting-state-fMRI were conducted. Amygdala-nuclei segmentation and amygdala-to-whole-brain FC analysis were performed. Linear mixed effects models and correlation analyses were conducted between FC, relVO2max, and mood scores. Data showed increases in relVO2max exclusively in the IG. Stronger anticorrelation in amygdala-precuneus FC was found, along with a stronger positive correlation in the amygdala-temporal pole FC in the IG after 4 and 6 months, while mood and amygdala volume did not reveal significant interactions. The relVO2max/amygdala-temporal pole FC correlated positively, and the amygdala-precuneus/amygdala-temporal pole FC correlated negatively. Findings suggest that exercise induced long-term modulations of the amygdala FC with the precuneus and temporal pole, shedding light on potential mechanisms by which exercise has positive influences on mood-related networks, typically altered in affective disorders.
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11
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Bayih SG, Jankiewicz M, Alhamud A, van der Kouwe AJW, Meintjes EM. Self-navigated prospective motion correction for 3D-EPI acquisition. Magn Reson Med 2022; 88:211-223. [PMID: 35344618 DOI: 10.1002/mrm.29202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/31/2021] [Accepted: 01/29/2022] [Indexed: 11/10/2022]
Abstract
PURPOSE Although 3D EPI is more susceptible to motion artifacts than 2D EPI, it presents some benefits for functional MRI, including the absence of spin-history artifacts, greater potential for parallel imaging acceleration, and better functional sensitivity in high-resolution imaging. Here we present a self-navigated 3D-EPI sequence suitable for prospective motion-corrected functional MRI without additional hardware or pulses. METHODS For each volume acquisition, the first 24 of the 52 partitions being acquired are accumulated to a new feedback block that was added to the image reconstruction pipeline. After zero-filling the remaining partitions, the feedback block constructs a volumetric self-navigator (vSNav), co-registers it to the reference vSNav acquired during the first volume acquisition, and sends motion estimates to the sequence. The sequence then updates its FOV and acquires subsequent partitions with the adjusted FOV, until the next update is received. The sequence was validated without and with intentional motion in phantom and in vivo on a 3T Skyra. RESULTS For phantom scans, the FOV was updated 0.704 s after acquisition of the vSNav partitions, and for in vivo scans after 0.768 s. Both phantom and in vivo data demonstrated stable motion estimates in the absence of motion. For in vivo acquisitions, prospective head-pose estimates using the vSNav's and retrospective estimates with FLIRT (FMRIB's Linear Image Registration Tool) agreed to within 0.23 mm (< 10% of the slice thickness) and 0.14° in all directions. CONCLUSION Depending when motion occurs during a volume acquisition, the proposed method fully corrects the FOV and recovers image quality within one volume acquisition.
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Affiliation(s)
- Samuel Getaneh Bayih
- Biomedical Engineering Research Center, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Marcin Jankiewicz
- Biomedical Engineering Research Center, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa.,Cape Universities Body Imaging Center, University of Cape Town, Cape Town, South Africa
| | - A Alhamud
- Biomedical Engineering Research Center, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa.,Cape Universities Body Imaging Center, University of Cape Town, Cape Town, South Africa.,The Modern Pioneer Center and ArSMRM for MRI Training and Development, Tripoli, Libya
| | - André J W van der Kouwe
- Biomedical Engineering Research Center, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa.,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ernesta M Meintjes
- Biomedical Engineering Research Center, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Cape Universities Body Imaging Center, University of Cape Town, Cape Town, South Africa
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12
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Lohner V, Enkirch SJ, Hattingen E, Stöcker T, Breteler MMB. Safety of Tattoos, Permanent Make-Up, and Medical Implants in Population-Based 3T Magnetic Resonance Brain Imaging: The Rhineland Study. Front Neurol 2022; 13:795573. [PMID: 35392639 PMCID: PMC8980837 DOI: 10.3389/fneur.2022.795573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Excluding persons from magnetic resonance imaging (MRI) research studies based on their medical history or because they have tattoos, can create bias and compromise the validity and generalizability of study results. In the population-based Rhineland Study, we limited exclusion criteria for MRI and allowed participants with passive medical implants, tattoos or permanent make-up to undergo MRI. Thereby, we could include 16.6% more people than would have been possible based on common recommendations. We observed no adverse events or artifacts. This supports that most passive medical implants, tattoos and permanent make-up are MRI suitable and can be scanned in research settings.
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Affiliation(s)
- Valerie Lohner
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Simon J. Enkirch
- Clinic for Neuroradiology, University Hospital Bonn, Bonn, Germany
| | - Elke Hattingen
- Clinic for Neuroradiology, University Hospital Bonn, Bonn, Germany
- Department of Neuroradiology, University Hospital Frankfurt, Frankfurt, Germany
| | - Tony Stöcker
- MR Physics, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Physics and Astronomy, University of Bonn, Bonn, Germany
| | - Monique M. B. Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
- *Correspondence: Monique M. B. Breteler
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13
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Schulze M, Aslan B, Stöcker T, Stirnberg R, Lux S, Philipsen A. Disentangling early versus late audiovisual integration in adult ADHD: a combined behavioural and resting-state connectivity study. J Psychiatry Neurosci 2021; 46:E528-E537. [PMID: 34548387 PMCID: PMC8526154 DOI: 10.1503/jpn.210017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/27/2021] [Accepted: 06/21/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Studies investigating sensory processing in attention-deficit/hyperactivity disorder (ADHD) have shown altered visual and auditory processing. However, evidence is lacking for audiovisual interplay - namely, multisensory integration. As well, neuronal dysregulation at rest (e.g., aberrant within- or between-network functional connectivity) may account for difficulties with integration across the senses in ADHD. We investigated whether sensory processing was altered at the multimodal level in adult ADHD and included resting-state functional connectivity to illustrate a possible overlap between deficient network connectivity and the ability to integrate stimuli. METHODS We tested 25 patients with ADHD and 24 healthy controls using 2 illusionary paradigms: the sound-induced flash illusion and the McGurk illusion. We applied the Mann-Whitney U test to assess statistical differences between groups. We acquired resting-state functional MRIs on a 3.0 T Siemens magnetic resonance scanner, using a highly accelerated 3-dimensional echo planar imaging sequence. RESULTS For the sound-induced flash illusion, susceptibility and reaction time were not different between the 2 groups. For the McGurk illusion, susceptibility was significantly lower for patients with ADHD, and reaction times were significantly longer. At a neuronal level, resting-state functional connectivity in the ADHD group was more highly regulated in polymodal regions that play a role in binding unimodal sensory inputs from different modalities and enabling sensory-to-cognition integration. LIMITATIONS We did not explicitly screen for autism spectrum disorder, which has high rates of comorbidity with ADHD and also involves impairments in multisensory integration. Although the patients were carefully screened by our outpatient department, we could not rule out the possibility of autism spectrum disorder in some participants. CONCLUSION Unimodal hypersensitivity seems to have no influence on the integration of basal stimuli, but it might have negative consequences for the multisensory integration of complex stimuli. This finding was supported by observations of higher resting-state functional connectivity between unimodal sensory areas and polymodal multisensory integration convergence zones for complex stimuli.
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Affiliation(s)
- Marcel Schulze
- From the Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany (Schulze, Aslan, Lux, Philipsen); Biopsychology and Cognitive Neuroscience, Faculty of Psychology and Sports Science, Bielefeld University, Bielefeld, Germany (Schulze); the German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany (Stöcker, Stirnberg); and the Department of Physics and Astronomy, University of Bonn, Bonn, Germany (Stöcker)
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14
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Raimondo L, Oliveira ĹAF, Heij J, Priovoulos N, Kundu P, Leoni RF, van der Zwaag W. Advances in resting state fMRI acquisitions for functional connectomics. Neuroimage 2021; 243:118503. [PMID: 34479041 DOI: 10.1016/j.neuroimage.2021.118503] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 01/21/2023] Open
Abstract
Resting state functional magnetic resonance imaging (rs-fMRI) is based on spontaneous fluctuations in the blood oxygen level dependent (BOLD) signal, which occur simultaneously in different brain regions, without the subject performing an explicit task. The low-frequency oscillations of the rs-fMRI signal demonstrate an intrinsic spatiotemporal organization in the brain (brain networks) that may relate to the underlying neural activity. In this review article, we briefly describe the current acquisition techniques for rs-fMRI data, from the most common approaches for resting state acquisition strategies, to more recent investigations with dedicated hardware and ultra-high fields. Specific sequences that allow very fast acquisitions, or multiple echoes, are discussed next. We then consider how acquisition methods weighted towards specific parts of the BOLD signal, like the Cerebral Blood Flow (CBF) or Volume (CBV), can provide more spatially specific network information. These approaches are being developed alongside the commonly used BOLD-weighted acquisitions. Finally, specific applications of rs-fMRI to challenging regions such as the laminae in the neocortex, and the networks within the large areas of subcortical white matter regions are discussed. We finish the review with recommendations for acquisition strategies for a range of typical applications of resting state fMRI.
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Affiliation(s)
- Luisa Raimondo
- Spinoza Centre for Neuroimaging, Amsterdam, the Netherlands; Experimental and Applied Psychology, VU University, Amsterdam, the Netherlands
| | - Ĺcaro A F Oliveira
- Spinoza Centre for Neuroimaging, Amsterdam, the Netherlands; Experimental and Applied Psychology, VU University, Amsterdam, the Netherlands
| | - Jurjen Heij
- Spinoza Centre for Neuroimaging, Amsterdam, the Netherlands; Experimental and Applied Psychology, VU University, Amsterdam, the Netherlands
| | | | - Prantik Kundu
- Hyperfine Research Inc, Guilford, CT, United States; Icahn School of Medicine at Mt. Sinai, New York, United States
| | - Renata Ferranti Leoni
- InBrain, Department of Physics, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil
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15
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Noble S, Scheinost D, Constable RT. A guide to the measurement and interpretation of fMRI test-retest reliability. Curr Opin Behav Sci 2021; 40:27-32. [PMID: 33585666 PMCID: PMC7875178 DOI: 10.1016/j.cobeha.2020.12.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The test-retest reliability of functional neuroimaging data has recently been a topic of much discussion. Despite early conflicting reports, converging reports now suggest that test-retest reliability is poor for standard univariate measures-namely, voxel- and region-level task-based activation and edge-level functional connectivity. To better understand the implications of these recent studies requires understanding the nuances of test-retest reliability as commonly measured by the intraclass correlation coefficient (ICC). Here we provide a guide to the measurement and interpretation of test-retest reliability in functional neuroimaging and review major findings in the literature. We highlight the importance of making choices that improve reliability so long as they do not diminish validity, pointing to the potential of multivariate approaches that improve both. Finally, we discuss the implications of recent reports of low test-retest reliability in the context of ongoing work in the field.
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Affiliation(s)
- Stephanie Noble
- Department of Radiology and Biomedical Imaging, Yale School of Medicine
| | - Dustin Scheinost
- Department of Radiology and Biomedical Imaging, Yale School of Medicine
- Department of Statistics and Data Science, Yale University
- Child Study Center, Yale School of Medicine
- Department of Biomedical Engineering, Yale School of Medicine
| | - R Todd Constable
- Department of Radiology and Biomedical Imaging, Yale School of Medicine
- Child Study Center, Yale School of Medicine
- Department of Biomedical Engineering, Yale School of Medicine
- Department of Neurosurgery, Yale School of Medicine
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16
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Bollmann S, Barth M. New acquisition techniques and their prospects for the achievable resolution of fMRI. Prog Neurobiol 2020; 207:101936. [PMID: 33130229 DOI: 10.1016/j.pneurobio.2020.101936] [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: 05/15/2020] [Revised: 09/10/2020] [Accepted: 10/18/2020] [Indexed: 01/17/2023]
Abstract
This work reviews recent advances in technologies for functional magnetic resonance imaging (fMRI) of the human brain and highlights the push for higher functional specificity based on increased spatial resolution and specific MR contrasts to reveal previously undetectable functional properties of small-scale cortical structures. We discuss how the combination of MR hardware, advanced acquisition techniques and various MR contrast mechanisms have enabled recent progress in functional neuroimaging. However, these advanced fMRI practices have only been applied to a handful of neuroscience questions to date, with the majority of the neuroscience community still using conventional imaging techniques. We thus discuss upcoming challenges and possibilities for fMRI technology development in human neuroscience. We hope that readers interested in functional brain imaging acquire an understanding of current and novel developments and potential future applications, even if they don't have a background in MR physics or engineering. We summarize the capabilities of standard fMRI acquisition schemes with pointers to relevant literature and comprehensive reviews and introduce more recent developments.
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Affiliation(s)
- Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Markus Barth
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia; School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Australia; ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, QLD, Australia.
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17
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Stirnberg R, Stöcker T. Segmented K-space blipped-controlled aliasing in parallel imaging for high spatiotemporal resolution EPI. Magn Reson Med 2020; 85:1540-1551. [PMID: 32936488 DOI: 10.1002/mrm.28486] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE A segmented k-space blipped-controlled aliasing in parallel imaging (skipped-CAIPI) sampling strategy for EPI is proposed, which allows for a flexible choice of EPI factor and phase encode bandwidth independent of the controlled aliasing in parallel imaging (CAIPI) sampling pattern. THEORY AND METHODS With previously proposed approaches, exactly two EPI trajectories were possible given a specific CAIPI pattern, either with slice gradient blips (blipped-CAIPI) or following a shot-selective CAIPI approach (higher resolution). Recently, interleaved multi-shot segmentation along shot-selective CAIPI trajectories has been applied for high-resolution anatomical imaging. For more flexibility and a broader range of applications, we propose segmentation along any blipped-CAIPI trajectory. Thus, all EPI factors and phase encode bandwidths available with traditional segmented EPI can be combined with controlled aliasing. RESULTS Temporal SNR maps of moderate-to-high-resolution time series acquisitions at varying undersampling factors demonstrate beneficial sampling alternatives to blipped-CAIPI or shot-selective CAIPI. Rapid high-resolution scans furthermore demonstrate SNR-efficient and motion-robust structural imaging with almost arbitrary EPI factor and minimal noise penalty. CONCLUSION Skipped-CAIPI sampling increases protocol flexibility for high spatiotemporal resolution EPI. In terms of SNR and efficiency, high-resolution functional or structural scans benefit vastly from a free choice of the CAIPI pattern. Even at moderate resolutions, the independence of sampling pattern, TE, and image matrix size is valuable for optimized functional protocol design. Although demonstrated with 3D-EPI, skipped-CAIPI is also applicable with simultaneous multislice EPI.
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Affiliation(s)
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Physics and Astronomy, University of Bonn, Bonn, Germany
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18
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Layer-dependent functional connectivity methods. Prog Neurobiol 2020; 207:101835. [DOI: 10.1016/j.pneurobio.2020.101835] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/30/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022]
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19
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Mueller S, Stirnberg R, Akbey S, Ehses P, Scheffler K, Stöcker T, Zaiss M. Whole brain snapshot CEST at 3T using 3D‐EPI: Aiming for speed, volume, and homogeneity. Magn Reson Med 2020; 84:2469-2483. [DOI: 10.1002/mrm.28298] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/16/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Sebastian Mueller
- High‐field Magnetic Resonance Center Max Planck Institute for Biological Cybernetics Tuebingen Germany
| | | | - Suzan Akbey
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - Philipp Ehses
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
| | - Klaus Scheffler
- High‐field Magnetic Resonance Center Max Planck Institute for Biological Cybernetics Tuebingen Germany
- Department of Biomedical Magnetic Resonance Eberhard Karls University Tuebingen Tuebingen Germany
| | - Tony Stöcker
- German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
- Department of Physics and Astronomy University of Bonn Bonn Germany
| | - Moritz Zaiss
- High‐field Magnetic Resonance Center Max Planck Institute for Biological Cybernetics Tuebingen Germany
- Department of Neuroradiology University Hospital Erlangen Erlangen Germany
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20
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Hendriks AD, D'Agata F, Raimondo L, Schakel T, Geerts L, Luijten PR, Klomp DW, Petridou N. Pushing functional MRI spatial and temporal resolution further: High-density receive arrays combined with shot-selective 2D CAIPIRINHA for 3D echo-planar imaging at 7 T. NMR IN BIOMEDICINE 2020; 33:e4281. [PMID: 32128898 PMCID: PMC7187278 DOI: 10.1002/nbm.4281] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 05/04/2023]
Abstract
To be able to examine dynamic and detailed brain functions, the spatial and temporal resolution of 7 T MRI needs to improve. In this study, it was investigated whether submillimeter multishot 3D EPI fMRI scans, acquired with high-density receive arrays, can benefit from a 2D CAIPIRINHA sampling pattern, in terms of noise amplification (g-factor), temporal SNR and fMRI sensitivity. High-density receive arrays were combined with a shot-selective 2D CAIPIRINHA implementation for multishot 3D EPI sequences at 7 T. In this implementation, in contrast to conventional inclusion of extra kz gradient blips, specific EPI shots are left out to create a CAIPIRINHA shift and reduction of scan time. First, the implementation of the CAIPIRINHA sequence was evaluated with a standard receive setup by acquiring submillimeter whole brain T2 *-weighted anatomy images. Second, the CAIPIRINHA sequence was combined with high-density receive arrays to push the temporal resolution of submillimeter 3D EPI fMRI scans of the visual cortex. Results show that the shot-selective 2D CAIPIRINHA sequence enables a reduction in scan time for 0.5 mm isotropic 3D EPI T2 *-weighted anatomy scans by a factor of 4 compared with earlier reports. The use of the 2D CAIPIRINHA implementation in combination with high-density receive arrays, enhances the image quality of submillimeter 3D EPI scans of the visual cortex at high acceleration as compared to conventional SENSE. Both the g-factor and temporal SNR improved, resulting in a method that is more sensitive to the fMRI signal. Using this method, it is possible to acquire submillimeter single volume 3D EPI scans of the visual cortex in a subsecond timeframe. Overall, high-density receive arrays in combination with shot-selective 2D CAIPIRINHA for 3D EPI scans prove to be valuable for reducing the scan time of submillimeter MRI acquisitions.
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Affiliation(s)
- Arjan D. Hendriks
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | - Federico D'Agata
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
- Department of NeuroscienceUniversity of TurinTurinItaly
| | - Luisa Raimondo
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
- Spinoza Centre for NeuroimagingAmsterdamthe Netherlands
| | - Tim Schakel
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | | | - Peter R. Luijten
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | - Dennis W.J. Klomp
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
| | - Natalia Petridou
- Department of RadiologyCenter for Image Sciences, University Medical Center UtrechtUtrechtthe Netherlands
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21
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Moeller S, Ramanna S, Lenglet C, Pisharady PK, Auerbach EJ, Delabarre L, Wu X, Akcakaya M, Ugurbil K. Self-navigation for 3D multishot EPI with data-reference. Magn Reson Med 2020; 84:1747-1762. [PMID: 32115756 DOI: 10.1002/mrm.28231] [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: 04/15/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 02/03/2023]
Abstract
PURPOSE In this study, we sought to develop a self-navigation strategy for improving the reconstruction of diffusion weighted 3D multishot echo planar imaging (EPI). We propose a method for extracting the phase correction information from the acquisition itself, eliminating the need for a 2D navigator, further accelerating the acquisition. METHODS In-vivo acquisitions at 3T with 0.9 mm and 1.5 mm isotropic resolutions were used to evaluate the performance of the self-navigation strategy. Sensitivity to motion was tested using a large difference in pitch position of the head. Using a multishell diffusion weighted acquisition, tractography results were obtained at (0.9 mm)3 to validate the quality with conventional acquisition. RESULTS The use of 3D multislab EPI with self-navigation enables 3D diffusion-weighted spin echo EPI acquisitions that have the same efficiency as 2D single-shot acquisition. For matched acquisition time the image signal-to-noise ratio (SNR) between 3D and 2D acquisition is shown to be comparable for whole-brain coverage with (1.5 mm)3 resolution and for (0.9 mm)3 resolution the 3D acquisition has higher SNR than what can be obtained with 2D acquisitions using current state-of-art multiband techniques. The self-navigation technique was shown to be stable under inter-volume motion. In tractography analysis, the higher resolution afforded by our technique enabled clear delineation of the tapetum and posterior corona radiata. CONCLUSION The proposed self-navigation approach utilized a self-consistent phase in 3D diffusion weighted acquisitions. Its efficiency and stability were demonstrated for a plurality of common acquisitions. The proposed self-navigation approach allows for faster acquisition of 3D multishot EPI desirable for large field of view and/or higher resolution.
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Affiliation(s)
- Steen Moeller
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Sudhir Ramanna
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Christophe Lenglet
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Pramod K Pisharady
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Edward J Auerbach
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Lance Delabarre
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Xiaoping Wu
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Mehmet Akcakaya
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kamil Ugurbil
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
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Prando G, Zorzi M, Bertoldo A, Corbetta M, Zorzi M, Chiuso A. Sparse DCM for whole-brain effective connectivity from resting-state fMRI data. Neuroimage 2020; 208:116367. [DOI: 10.1016/j.neuroimage.2019.116367] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
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Norbeck O, Sprenger T, Avventi E, Rydén H, Kits A, Berglund J, Skare S. Optimizing 3D EPI for rapid T
1
‐weighted imaging. Magn Reson Med 2020; 84:1441-1455. [DOI: 10.1002/mrm.28222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/14/2020] [Accepted: 01/29/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Ola Norbeck
- Department of Neuroradiology Karolinska University Hospital Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Tim Sprenger
- MR Applied Science Laboratory Europe, GE Healthcare Stockholm Sweden
| | - Enrico Avventi
- Department of Neuroradiology Karolinska University Hospital Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Henric Rydén
- Department of Neuroradiology Karolinska University Hospital Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Annika Kits
- Department of Neuroradiology Karolinska University Hospital Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Johan Berglund
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
| | - Stefan Skare
- Department of Neuroradiology Karolinska University Hospital Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
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Noble S, Scheinost D, Constable RT. A decade of test-retest reliability of functional connectivity: A systematic review and meta-analysis. Neuroimage 2019; 203:116157. [PMID: 31494250 PMCID: PMC6907736 DOI: 10.1016/j.neuroimage.2019.116157] [Citation(s) in RCA: 308] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Once considered mere noise, fMRI-based functional connectivity has become a major neuroscience tool in part due to early studies demonstrating its reliability. These fundamental studies revealed only the tip of the iceberg; over the past decade, many test-retest reliability studies have continued to add nuance to our understanding of this complex topic. A summary of these diverse and at times contradictory perspectives is needed. OBJECTIVES We aimed to summarize the existing knowledge regarding test-retest reliability of functional connectivity at the most basic unit of analysis: the individual edge level. This entailed (1) a meta-analytic estimate of reliability and (2) a review of factors influencing reliability. METHODS A search of Scopus was conducted to identify studies that estimated edge-level test-retest reliability. To facilitate comparisons across studies, eligibility was restricted to studies measuring reliability via the intraclass correlation coefficient (ICC). The meta-analysis included a random effects pooled estimate of mean edge-level ICC, with studies nested within datasets. The review included a narrative summary of factors influencing edge-level ICC. RESULTS From an initial pool of 212 studies, 44 studies were identified for the qualitative review and 25 studies for quantitative meta-analysis. On average, individual edges exhibited a "poor" ICC of 0.29 (95% CI = 0.23 to 0.36). The most reliable measurements tended to involve: (1) stronger, within-network, cortical edges, (2) eyes open, awake, and active recordings, (3) more within-subject data, (4) shorter test-retest intervals, (5) no artifact correction (likely due in part to reliable artifact), and (6) full correlation-based connectivity with shrinkage. CONCLUSION This study represents the first meta-analysis and systematic review investigating test-retest reliability of edge-level functional connectivity. Key findings suggest there is room for improvement, but care should be taken to avoid promoting reliability at the expense of validity. By pooling existing knowledge regarding this key facet of accuracy, this study supports broader efforts to improve inferences in the field.
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Affiliation(s)
- Stephanie Noble
- Interdepartmental Neuroscience Program, Yale University, USA.
| | - Dustin Scheinost
- Interdepartmental Neuroscience Program, Yale University, USA; Department of Radiology and Biomedical Imaging, Yale School of Medicine, USA; Department of Statistics and Data Science, Yale University, USA; Child Study Center, Yale School of Medicine, USA
| | - R Todd Constable
- Interdepartmental Neuroscience Program, Yale University, USA; Department of Radiology and Biomedical Imaging, Yale School of Medicine, USA; Department of Neurosurgery, Yale School of Medicine, USA
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25
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Comparison of SMS-EPI and 3D-EPI at 7T in an fMRI localizer study with matched spatiotemporal resolution and homogenized excitation profiles. PLoS One 2019; 14:e0225286. [PMID: 31751410 PMCID: PMC6872176 DOI: 10.1371/journal.pone.0225286] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023] Open
Abstract
The simultaneous multi-slice EPI (SMS-EPI, a.k.a. MB-EPI) sequence has met immense popularity recently in functional neuroimaging. A still less common alternative is the use of 3D-EPI, which offers similar acceleration capabilities. The aim of this work was to compare the SMS-EPI and the 3D-EPI sequences in terms of sampling strategies for the detection of task-evoked activations at 7T using detection theory. To this end, the spatial and temporal resolutions of the sequences were matched (1.6 mm isotropic resolution, TR = 1200 ms) and their excitation profiles were homogenized by means of calibration-free parallel-transmission (Universal Pulses). We used a fast-event “localizer” paradigm of 5:20 min in order to probe sensorimotor functions (visual, auditory and motor tasks) as well as higher level functions (language comprehension, mental calculation), where results from a previous large-scale study at 3T (N = 81) served as ground-truth reference for the brain areas implicated in each cognitive function. In the current study, ten subjects were scanned while their activation maps were generated for each cognitive function with the GLM analysis. The SMS-EPI and 3D-EPI sequences were compared in terms of raw tSNR, t-score testing for the mean signal, activation strength and accuracy of the robust sensorimotor functions. To this end, the sensitivity and specificity of these contrasts were computed by comparing their activation maps to the reference brain areas obtained in the 3T study. Estimated flip angle distributions in the brain reported a normalized root mean square deviation from the target value below 10% for both sequences. The analysis of the t-score testing for the mean signal revealed temporal noise correlations, suggesting the use of this metric instead of the traditional tSNR for testing fMRI sequences. The SMS-EPI and 3D-EPI thereby yielded similar performance from a detection theory perspective.
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26
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Luo T, Noll DC, Fessler JA, Nielsen JF. A GRAPPA algorithm for arbitrary 2D/3D non-Cartesian sampling trajectories with rapid calibration. Magn Reson Med 2019; 82:1101-1112. [PMID: 31050011 DOI: 10.1002/mrm.27801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/03/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE GRAPPA is a popular reconstruction method for Cartesian parallel imaging, but is not easily extended to non-Cartesian sampling. We introduce a general and practical GRAPPA algorithm for arbitrary non-Cartesian imaging. METHODS We formulate a general GRAPPA reconstruction by associating a unique kernel with each unsampled k-space location with a distinct constellation, that is, local sampling pattern. We calibrate these generalized kernels using the Fourier transform phase shift property applied to fully gridded or separately acquired Cartesian Autocalibration signal (ACS) data. To handle the resulting large number of different kernels, we introduce a fast calibration algorithm based on nonuniform FFT (NUFFT) and adoption of circulant ACS boundary conditions. We applied our method to retrospectively under-sampled rotated stack-of-stars/spirals in vivo datasets, and to a prospectively under-sampled rotated stack-of-spirals functional MRI acquisition with a finger-tapping task. RESULTS We reconstructed all datasets without performing any trajectory-specific manual adaptation of the method. For the retrospectively under-sampled experiments, our method achieved image quality (i.e., error and g-factor maps) comparable to conjugate gradient SENSE (cg-SENSE) and SPIRiT. Functional activation maps obtained from our method were in good agreement with those obtained using cg-SENSE, but required a shorter total reconstruction time (for the whole time-series): 3 minutes (proposed) vs 15 minutes (cg-SENSE). CONCLUSIONS This paper introduces a general 3D non-Cartesian GRAPPA that is fast enough for practical use on today's computers. It is a direct generalization of original GRAPPA to non-Cartesian scenarios. The method should be particularly useful in dynamic imaging where a large number of frames are reconstructed from a single set of ACS data.
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Affiliation(s)
- Tianrui Luo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Douglas C Noll
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey A Fessler
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jon-Fredrik Nielsen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
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Meineke J, Nielsen T. Data consistency-driven determination of B 0 -fluctuations in gradient-echo MRI. Magn Reson Med 2018; 81:3046-3055. [PMID: 30515876 DOI: 10.1002/mrm.27630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023]
Abstract
PURPOSE Introduce a method to estimate B 0 -fluctuations based on the analysis of raw k-space data, without sequence modifications or external hardware, and correct for their detrimental effects in gradient-echo MRI. THEORY Inconsistencies in multi-channel raw k-space data can be used to estimate B 0 -fluctuations by exploiting coil-sensitivity information. METHODS The proposed method, dubbed consistency navigation, is used to extract B 0 -fluctuations from T 2 * -weighted 3D gradient-echo data. These results are compared with the results from an MR phase navigator and respiratory bellows. The spatial variation of the B 0 -fluctuation amplitude is derived using the sensitivity maps of the coil array and compared with direct measurements based on dynamic 2D gradient-echo data. RESULTS B 0 -fluctuations derived from the consistency navigator and MR phase navigator are highly correlated. Images corrected for these fluctuations show marked improvements in homogeneity and tissue delineation. The spatial variation of the B 0 -fluctuation amplitude follows closely the variation directly measured from time-resolved 2D scans. CONCLUSIONS Based on the consistency navigator, an accurate estimation of the spatiotemporal characteristics of B 0 -fluctuations and correction of T 2 * -weighted images has been demonstrated.
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Boillat Y, Zwaag W. Whole brain measurements of the positive BOLD response variability during a finger tapping task at 7 T show regional differences in its profiles. Magn Reson Med 2018; 81:2720-2727. [DOI: 10.1002/mrm.27566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Yohan Boillat
- Laboratory for Functional and Metabolic Imaging Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland
| | - Wietske Zwaag
- Biomedical Imaging Research Center Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland
- Spinoza Centre for Neuroimaging Amsterdam Netherlands
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Rettenmeier C, Maziero D, Qian Y, Stenger VA. A circular echo planar sequence for fast volumetric fMRI. Magn Reson Med 2018; 81:1685-1698. [PMID: 30273963 DOI: 10.1002/mrm.27522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/03/2018] [Accepted: 08/15/2018] [Indexed: 11/07/2022]
Abstract
PURPOSE To demonstrate a circular EPI (CEPI) sequence as well as a generalized EPI reconstruction for fast fMRI with parallel imaging acceleration. METHODS The CEPI acquisition was constructed using variable readout lengths and maximum ramp sampling as well as blipped-CAIPI z-gradient encoding for simultaneous multislice (SMS) and 3D volumetric imaging. A signal equation model with constant and linear phase terms was used to iteratively reconstruct images with low ghosting. Simulation, phantom, and human imaging experiments including audio/visual fMRI were performed at 3T using a 52-channel coil. RESULTS Application of CEPI gradients with duration of 27 ms covering a 22-cm FOV at a 64 × 64 pixel resolution in SMS and 3D acquisitions resulted in images with comparable quality to those of standard Cartesian EPI. With parallel imaging techniques robust detection of BOLD fMRI activation with temporal sampling down to 275 ms was possible. The high temporal resolution enabled higher activation statistics at a penalty in increased noise and residual aliasing. The un-accelerated 3D acquisition showed large temporal instability compared with a standard 2D acquisition. CONCLUSION Nonuniform sampling and generalized image reconstructions can be applied to EPI acquisitions including those with blipped-CAIPI z gradients. The same gradients can be used for either SMS or 3D acquisitions providing identical coverage.
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Affiliation(s)
- Christoph Rettenmeier
- Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Danilo Maziero
- Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Yongxian Qian
- Department of Radiology, New York University School of Medicine, New York, New York
| | - V Andrew Stenger
- Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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Frässle S, Lomakina EI, Kasper L, Manjaly ZM, Leff A, Pruessmann KP, Buhmann JM, Stephan KE. A generative model of whole-brain effective connectivity. Neuroimage 2018; 179:505-529. [DOI: 10.1016/j.neuroimage.2018.05.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022] Open
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Sati P. Diagnosis of multiple sclerosis through the lens of ultra-high-field MRI. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 291:101-109. [PMID: 29705032 PMCID: PMC6022748 DOI: 10.1016/j.jmr.2018.01.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
The long-standing relationship between ultra-high-field (7 T) MRI and multiple sclerosis (MS) has brought new insights to our understanding of lesion evolution and its associated pathology. With the recent FDA approval of a commercially available scanner, 7 T MRI is finally entering the clinic with great expectations about its potential added value. By looking through the prism of MS diagnosis, this perspective article discusses current limitations and prospects of 7 T MRI techniques relevant to helping clinicians diagnose patients encountered in daily practice.
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Affiliation(s)
- Pascal Sati
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Drive MSC 1400, Building 10 Room 5C103, Bethesda, MD 20852, USA.
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Bright MG, Croal PL, Blockley NP, Bulte DP. Multiparametric measurement of cerebral physiology using calibrated fMRI. Neuroimage 2017; 187:128-144. [PMID: 29277404 DOI: 10.1016/j.neuroimage.2017.12.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023] Open
Abstract
The ultimate goal of calibrated fMRI is the quantitative imaging of oxygen metabolism (CMRO2), and this has been the focus of numerous methods and approaches. However, one underappreciated aspect of this quest is that in the drive to measure CMRO2, many other physiological parameters of interest are often acquired along the way. This can significantly increase the value of the dataset, providing greater information that is clinically relevant, or detail that can disambiguate the cause of signal variations. This can also be somewhat of a double-edged sword: calibrated fMRI experiments combine multiple parameters into a physiological model that requires multiple steps, thereby providing more opportunity for error propagation and increasing the noise and error of the final derived values. As with all measurements, there is a trade-off between imaging time, spatial resolution, coverage, and accuracy. In this review, we provide a brief overview of the benefits and pitfalls of extracting multiparametric measurements of cerebral physiology through calibrated fMRI experiments.
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Affiliation(s)
- Molly G Bright
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK; Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Paula L Croal
- IBME, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Nicholas P Blockley
- FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Daniel P Bulte
- IBME, Department of Engineering Science, University of Oxford, Oxford, UK; FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
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