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Park S, Beckett A, Häkkinen S, Walker E, Ma SJ, Kim S, Kim H, Feinberg DA. Higher spatial resolution and sensitivity in whole brain functional MRI at 7T using 3D EPI accelerated with variable density CAIPI sampling and temporal random walk. Magn Reson Med 2025. [PMID: 40275620 DOI: 10.1002/mrm.30512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 02/25/2025] [Accepted: 03/11/2025] [Indexed: 04/26/2025]
Abstract
PURPOSE To develop an efficient 3D EPI encoding technique for high spatiotemporal resolution functional MRI. METHODS To exploit spatiotemporal fMRI data structure, we introduce a variable density 2D CAIPI sampling in the spatial domain combined with time-wise extra random encoding in the time domain, thus achieving pseudo-regular sampling with a regular blip while allowing incoherent sampling in a complementary manner across time. This enabled temporally regularized reconstruction of highly accelerated functional data acquisition. The encoding scheme was then validated against temporally invariant CAIPI encoding by applying to locally confined and whole-brain around the primary visual cortex, respectively, with increasing the spatial resolutions. RESULTS For partial brain imaging, our proposed method achieved higher reconstruction accuracy, resulting in a substantial increase of SSIM compared to an alternative method for 0.64 mm-isotropic resolution. When used for whole brain imaging at 0.56 mm-isotropic resolution, our method showed a decreased spatial extent of activation and produced high-quality images for a clear distinction between activated and non-activated regions around calcarine fissure with high spatial specificity. CONCLUSION The proposed 3D EPI encoding scheme, which exploits coherent and incoherent sampling properties, can significantly improve the image quality while providing a good balance between sensitivity and specificity in the activated regions.
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Affiliation(s)
- Suhyung Park
- Department of Intelligent Electronics and Computer Engineering, Chonnam National University, Gwangju, Republic of Korea
| | - Alexander Beckett
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
- Advanced MRI Technologies, Sebastopol, California, USA
| | - Suvi Häkkinen
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - Erica Walker
- Advanced MRI Technologies, Sebastopol, California, USA
| | - Samantha J Ma
- Siemens Medical Solutions, USA, Inc., Berkeley, California, USA
| | - Sugil Kim
- Siemens Healthineers Ltd., Seoul, Republic of Korea
| | - Hahnsung Kim
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - David A Feinberg
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
- Advanced MRI Technologies, Sebastopol, California, USA
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2
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Posse S, Ramanna S, Moeller S, Vakamudi K, Otazo R, Sa de La Rocque Guimaraes B, Mullen M, Yacoub E. Real-time fMRI using multi-band echo-volumar imaging with millimeter spatial resolution and sub-second temporal resolution at 3 tesla. Front Neurosci 2025; 19:1543206. [PMID: 40143844 PMCID: PMC11936983 DOI: 10.3389/fnins.2025.1543206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 02/25/2025] [Indexed: 03/28/2025] Open
Abstract
Purpose In this study we develop undersampled echo-volumar imaging (EVI) using multi-band/simultaneous multi-slab encoding in conjunction with multi-shot slab-segmentation to accelerate 3D encoding and to reduce the duration of EVI encoding within slabs. This approach combines the sampling efficiency of single-shot 3D encoding with the sensitivity advantage of multi-echo acquisition. We describe the pulse sequence development and characterize the spatial-temporal resolution limits and BOLD sensitivity of this approach for high-speed task-based and resting-state fMRI at 3 T. We study the feasibility of further acceleration using compressed sensing (CS) and assess compatibility with NORDIC denoising. Methods Multi-band echo volumar imaging (MB-EVI) combines multi-band encoding of up to 6 slabs with CAIPI shifting, accelerated EVI encoding within slabs using up to 4-fold GRAPPA accelerations, 2-shot kz-segmentation and partial Fourier acquisitions along the two phase-encoding dimensions. Task-based and resting-state fMRI at 3 Tesla was performed across a range of voxel sizes (between 1 and 3 mm isotropic), repetition times (118-650 ms), and number of slabs (up to 12). MB-EVI was compared with multi-slab EVI (MS-EVI) and multi-band-EPI (MB-EPI). Results Image quality and temporal SNR of MB-EVI was comparable to MS-EVI when using 2-3 mm spatial resolution. High sensitivity for mapping task-based activation and resting-state connectivity at short TR was measured. Online deconvolution of T2* signal decay markedly reduced spatial blurring and improved image contrast. The high temporal resolution of MB-EVI enabled sensitive mapping of high-frequency resting-state connectivity above 0.3 Hz with 3 mm isotropic voxel size (TR: 163 ms). Detection of task-based activation with 1 mm isotropic voxel size was feasible in scan times as short as 1 min 13 s. Compressed sensing with up to 2.4-fold retrospective undersampling showed negligible loss in image quality and moderate region-specific losses in BOLD sensitivity. NORDIC denoising significantly enhanced fMRI sensitivity without introducing image blurring. Conclusion Combining MS-EVI with multi-band encoding enables high overall acceleration factors and provides flexibility for maximizing spatial-temporal resolution and volume coverage. The high BOLD sensitivity of this hybrid MB-EVI approach and its compatibility with online image reconstruction enables high spatial-temporal resolution real-time task-based and resting state fMRI.
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Affiliation(s)
- Stefan Posse
- Department of Neurology, University of New Mexico, Albuquerque, NM, United States
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, United States
| | - Sudhir Ramanna
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, United States
| | - Steen Moeller
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, United States
| | - Kishore Vakamudi
- Department of Neurology, University of New Mexico, Albuquerque, NM, United States
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, United States
| | - Ricardo Otazo
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Bruno Sa de La Rocque Guimaraes
- Department of Neurology, University of New Mexico, Albuquerque, NM, United States
- Department of Nuclear Engineering, University of New Mexico, Albuquerque, NM, United States
| | - Michael Mullen
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, United States
| | - Essa Yacoub
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, United States
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Kiersnowski OC, Fuchs P, Wastling SJ, Nassar J, Thornton JS, Shmueli K. Multiband accelerated 2D EPI for multi-echo brain QSM at 3 T. Magn Reson Med 2025; 93:183-198. [PMID: 39164832 DOI: 10.1002/mrm.30267] [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: 03/26/2024] [Revised: 06/26/2024] [Accepted: 08/05/2024] [Indexed: 08/22/2024]
Abstract
PURPOSE Data for QSM are typically acquired using multi-echo 3D gradient echo (GRE), but EPI can be used to accelerate QSM and provide shorter acquisition times. So far, EPI-QSM has been limited to single-echo acquisitions, which, for 3D GRE, are known to be less accurate than multi-echo sequences. Therefore, we compared single-echo and multi-echo EPI-QSM reconstructions across a range of parallel imaging and multiband acceleration factors. METHODS Using 2D single-shot EPI in the brain, we compared QSM from single-echo and multi-echo acquisitions across combined parallel-imaging and multiband acceleration factors ranging from 2 to 16, with volume pulse TRs from 21.7 to 3.2 s, respectively. For single-echo versus multi-echo reconstructions, we investigated the effect of acceleration factors on regional susceptibility values, temporal noise, and image quality. We introduce a novel masking method based on thresholding the magnitude of the local field gradients to improve brain masking in challenging regions. RESULTS At 1.6-mm isotropic resolution, high-quality QSM was achieved using multi-echo 2D EPI with a combined acceleration factor of 16 and a TR of 3.2 s, which enables functional applications. With these high acceleration factors, single-echo reconstructions are inaccurate and artefacted, rendering them unusable. Multi-echo acquisitions greatly improve QSM quality, particularly at higher acceleration factors, provide more consistent regional susceptibility values across acceleration factors, and decrease temporal noise compared with single-echo QSM reconstructions. CONCLUSION Multi-echo acquisition is more robust for EPI-QSM across parallel imaging and multiband acceleration factors than single-echo acquisition. Multi-echo EPI can be used for highly accelerated acquisition while preserving QSM accuracy and quality relative to gold-standard 3D-GRE QSM.
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Affiliation(s)
- Oliver C Kiersnowski
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Neuroradiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Patrick Fuchs
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Stephen J Wastling
- Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology, London, UK
| | - Jannette Nassar
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - John S Thornton
- Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, London, UK
- Lysholm Department of Neuroradiology, London, UK
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
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Cash RFH, Zalesky A. Personalized and Circuit-Based Transcranial Magnetic Stimulation: Evidence, Controversies, and Opportunities. Biol Psychiatry 2024; 95:510-522. [PMID: 38040047 DOI: 10.1016/j.biopsych.2023.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/03/2023]
Abstract
The development of neuroimaging methodologies to map brain connectivity has transformed our understanding of psychiatric disorders, the distributed effects of brain stimulation, and how transcranial magnetic stimulation can be best employed to target and ameliorate psychiatric symptoms. In parallel, neuroimaging research has revealed that higher-order brain regions such as the prefrontal cortex, which represent the most common therapeutic brain stimulation targets for psychiatric disorders, show some of the highest levels of interindividual variation in brain connectivity. These findings provide the rationale for personalized target site selection based on person-specific brain network architecture. Recent advances have made it possible to determine reproducible personalized targets with millimeter precision in clinically tractable acquisition times. These advances enable the potential advantages of spatially personalized transcranial magnetic stimulation targeting to be evaluated and translated to basic and clinical applications. In this review, we outline the motivation for target site personalization, preliminary support (mostly in depression), convergent evidence from other brain stimulation modalities, and generalizability beyond depression and the prefrontal cortex. We end by detailing methodological recommendations, controversies, and notable alternatives. Overall, while this research area appears highly promising, the value of personalized targeting remains unclear, and dedicated large prospective randomized clinical trials using validated methodology are critical.
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Affiliation(s)
- Robin F H Cash
- Melbourne Neuropsychiatry Centre and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia.
| | - Andrew Zalesky
- Melbourne Neuropsychiatry Centre and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia
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Yun SD, Küppers F, Shah NJ. Submillimeter fMRI Acquisition Techniques for Detection of Laminar and Columnar Level Brain Activation. J Magn Reson Imaging 2024; 59:747-766. [PMID: 37589385 DOI: 10.1002/jmri.28911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Since the first demonstration in the early 1990s, functional MRI (fMRI) has emerged as one of the most powerful, noninvasive neuroimaging tools to probe brain functions. Subsequently, fMRI techniques have advanced remarkably, enabling the acquisition of functional signals with a submillimeter voxel size. This innovation has opened the possibility of investigating subcortical neural activities with respect to the cortical depths or cortical columns. For this purpose, numerous previous works have endeavored to design suitable functional contrast mechanisms and dedicated imaging techniques. Depending on the choice of the functional contrast, functional signals can be detected with high sensitivity or with improved spatial specificity to the actual activation site, and the pertaining issues have been discussed in a number of earlier works. This review paper primarily aims to provide an overview of the subcortical fMRI techniques that allow the acquisition of functional signals with a submillimeter resolution. Here, the advantages and disadvantages of the imaging techniques will be described and compared. We also summarize supplementary imaging techniques that assist in the analysis of the subcortical brain activation for more accurate mapping with reduced geometric deformation. This review suggests that there is no single universally accepted method as the gold standard for subcortical fMRI. Instead, the functional contrast and the corresponding readout imaging technique should be carefully determined depending on the purpose of the study. Due to the technical limitations of current fMRI techniques, most subcortical fMRI studies have only targeted partial brain regions. As a future prospect, the spatiotemporal resolution of fMRI will be pushed to satisfy the community's need for a deeper understanding of whole-brain functions and the underlying connectivity in order to achieve the ultimate goal of a time-resolved and layer-specific spatial scale. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 1.
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Affiliation(s)
- Seong Dae Yun
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
| | - Fabian Küppers
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
- RWTH Aachen University, Aachen, Germany
- Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany
| | - N Jon Shah
- Institute of Neuroscience and Medicine 4, INM-4, Forschungszentrum Jülich, Jülich, Germany
- Institute of Neuroscience and Medicine 11, INM-11, JARA, Forschungszentrum Jülich, Jülich, Germany
- JARA - BRAIN - Translational Medicine, Aachen, Germany
- Department of Neurology, RWTH Aachen University, Aachen, Germany
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Beckers AB, Drenthen GS, Jansen JFA, Backes WH, Poser BA, Keszthelyi D. Comparing the efficacy of data-driven denoising methods for a multi-echo fMRI acquisition at 7T. Neuroimage 2023; 280:120361. [PMID: 37669723 DOI: 10.1016/j.neuroimage.2023.120361] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/16/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023] Open
Abstract
In functional magnetic resonance imaging (fMRI) of the brain the measured signal is corrupted by several (e.g. physiological, motion, and thermal) noise sources and depends on the image acquisition. Imaging at ultrahigh field strength is becoming increasingly popular as it offers increased spatial accuracy. The latter is of particular benefit in brainstem neuroimaging given the small cross-sectional area of most nuclei. However, physiological noise scales with field strength in fMRI acquisitions. Although this problem is in part solved by decreasing voxel size, it is clear that adequate physiological denoising is of utmost importance in brainstem-focused fMRI experiments. Multi-echo sequences have been reported to facilitate highly effective denoising through TE-dependence of Blood Oxygen Level Dependent (BOLD) signals, in a denoising method referred to as multi-echo independent component analysis (ME-ICA). It has not been explored previously how ME-ICA compares to other data-driven denoising approaches at ultrahigh field strength. In the current study, we compared the efficacy of several denoising methods, including anatomical component based correction (aCompCor), Automatic Removal of Motion Artifacts (ICA-AROMA) aggressive and non-aggressive options, ME-ICA, and a combination of ME-ICA and aCompCor. We assessed several data quality metrics, including temporal signal-to-noise ratio (tSNR), delta variation signal (DVARS), spectral density of the global signal, functional connectivity and Shannon spectral entropy. Moreover, we looked at the ability of each method to uncouple the global signal and respiration. In line with previous reports at lower field strengths, we demonstrate that after applying ME-ICA, the data is best post-processed in order to remove spatially diffuse noise with a method such as aCompCor. Our findings indicate that ME-ICA combined with aCompCor and the aggressive option of ICA-AROMA are highly effective denoising approaches for multi-echo data acquired at 7T. ME-ICA combined with aCompCor potentially preserves more signal-of-interest as compared to the aggressive option of ICA-AROMA.
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Affiliation(s)
- Abraham B Beckers
- Department of Internal Medicine, Division of Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Gerhard S Drenthen
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, PO Box 5800, Maastricht 6202 AZ, the Netherlands.
| | - Jacobus F A Jansen
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, PO Box 5800, Maastricht 6202 AZ, the Netherlands
| | - Walter H Backes
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, PO Box 5800, Maastricht 6202 AZ, the Netherlands
| | - Benedikt A Poser
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Daniel Keszthelyi
- Department of Internal Medicine, Division of Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
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Lloyd B, de Voogd LD, Mäki-Marttunen V, Nieuwenhuis S. Pupil size reflects activation of subcortical ascending arousal system nuclei during rest. eLife 2023; 12:e84822. [PMID: 37367220 PMCID: PMC10299825 DOI: 10.7554/elife.84822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Neuromodulatory nuclei that are part of the ascending arousal system (AAS) play a crucial role in regulating cortical state and optimizing task performance. Pupil diameter, under constant luminance conditions, is increasingly used as an index of activity of these AAS nuclei. Indeed, task-based functional imaging studies in humans have begun to provide evidence of stimulus-driven pupil-AAS coupling. However, whether there is such a tight pupil-AAS coupling during rest is not clear. To address this question, we examined simultaneously acquired resting-state fMRI and pupil-size data from 74 participants, focusing on six AAS nuclei: the locus coeruleus, ventral tegmental area, substantia nigra, dorsal and median raphe nuclei, and cholinergic basal forebrain. Activation in all six AAS nuclei was optimally correlated with pupil size at 0-2 s lags, suggesting that spontaneous pupil changes were almost immediately followed by corresponding BOLD-signal changes in the AAS. These results suggest that spontaneous changes in pupil size that occur during states of rest can be used as a noninvasive general index of activity in AAS nuclei. Importantly, the nature of pupil-AAS coupling during rest appears to be vastly different from the relatively slow canonical hemodynamic response function that has been used to characterize task-related pupil-AAS coupling.
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Affiliation(s)
- Beth Lloyd
- Institute of Psychology, Leiden UniversityLeidenNetherlands
| | - Lycia D de Voogd
- Donders Institute, Centre for Cognitive Neuroimaging, Radboud University NijmegenNijmegenNetherlands
- Behavioural Science Institute, Radboud UniversityNijmegenNetherlands
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Errante A, Gerbella M, Mingolla GP, Fogassi L. Activation of Cerebellum, Basal Ganglia and Thalamus During Observation and Execution of Mouth, hand, and foot Actions. Brain Topogr 2023:10.1007/s10548-023-00960-1. [PMID: 37133782 DOI: 10.1007/s10548-023-00960-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Humans and monkey studies showed that specific sectors of cerebellum and basal ganglia activate not only during execution but also during observation of hand actions. However, it is unknown whether, and how, these structures are engaged during the observation of actions performed by effectors different from the hand. To address this issue, in the present fMRI study, healthy human participants were required to execute or to observe grasping acts performed with different effectors, namely mouth, hand, and foot. As control, participants executed and observed simple movements performed with the same effectors. The results show that: (1) execution of goal-directed actions elicited somatotopically organized activations not only in the cerebral cortex but also in the cerebellum, basal ganglia, and thalamus; (2) action observation evoked cortical, cerebellar and subcortical activations, lacking a clear somatotopic organization; (3) in the territories displaying shared activations between execution and observation, a rough somatotopy could be revealed in both cortical, cerebellar and subcortical structures. The present study confirms previous findings that action observation, beyond the cerebral cortex, also activates specific sectors of cerebellum and subcortical structures and it shows, for the first time, that these latter are engaged not only during hand actions observation but also during the observation of mouth and foot actions. We suggest that each of the activated structures processes specific aspects of the observed action, such as performing internal simulation (cerebellum) or recruiting/inhibiting the overt execution of the observed action (basal ganglia and sensory-motor thalamus).
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Affiliation(s)
- Antonino Errante
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125, Parma, Italy
- Department of Diagnostics, Neuroradiology unit, University Hospital of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Marzio Gerbella
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125, Parma, Italy
| | - Gloria P Mingolla
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Piazzale Ludovico Antonio Scuro 10, 37124, Verona, Italy
| | - Leonardo Fogassi
- Department of Medicine and Surgery, University of Parma, Via Volturno 39, 43125, Parma, Italy.
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Ehrenberg AJ, Kelberman MA, Liu KY, Dahl MJ, Weinshenker D, Falgàs N, Dutt S, Mather M, Ludwig M, Betts MJ, Winer JR, Teipel S, Weigand AJ, Eschenko O, Hämmerer D, Leiman M, Counts SE, Shine JM, Robertson IH, Levey AI, Lancini E, Son G, Schneider C, Egroo MV, Liguori C, Wang Q, Vazey EM, Rodriguez-Porcel F, Haag L, Bondi MW, Vanneste S, Freeze WM, Yi YJ, Maldinov M, Gatchel J, Satpati A, Babiloni C, Kremen WS, Howard R, Jacobs HIL, Grinberg LT. Priorities for research on neuromodulatory subcortical systems in Alzheimer's disease: Position paper from the NSS PIA of ISTAART. Alzheimers Dement 2023; 19:2182-2196. [PMID: 36642985 PMCID: PMC10182252 DOI: 10.1002/alz.12937] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 01/17/2023]
Abstract
The neuromodulatory subcortical system (NSS) nuclei are critical hubs for survival, hedonic tone, and homeostasis. Tau-associated NSS degeneration occurs early in Alzheimer's disease (AD) pathogenesis, long before the emergence of pathognomonic memory dysfunction and cortical lesions. Accumulating evidence supports the role of NSS dysfunction and degeneration in the behavioral and neuropsychiatric manifestations featured early in AD. Experimental studies even suggest that AD-associated NSS degeneration drives brain neuroinflammatory status and contributes to disease progression, including the exacerbation of cortical lesions. Given the important pathophysiologic and etiologic roles that involve the NSS in early AD stages, there is an urgent need to expand our understanding of the mechanisms underlying NSS vulnerability and more precisely detail the clinical progression of NSS changes in AD. Here, the NSS Professional Interest Area of the International Society to Advance Alzheimer's Research and Treatment highlights knowledge gaps about NSS within AD and provides recommendations for priorities specific to clinical research, biomarker development, modeling, and intervention. HIGHLIGHTS: Neuromodulatory nuclei degenerate in early Alzheimer's disease pathological stages. Alzheimer's pathophysiology is exacerbated by neuromodulatory nuclei degeneration. Neuromodulatory nuclei degeneration drives neuropsychiatric symptoms in dementia. Biomarkers of neuromodulatory integrity would be value-creating for dementia care. Neuromodulatory nuclei present strategic prospects for disease-modifying therapies.
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Affiliation(s)
- Alexander J Ehrenberg
- Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Michael A Kelberman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kathy Y Liu
- Division of Psychiatry, University College London, London, UK
| | - Martin J Dahl
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Neus Falgàs
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Global Brain Health Institute, University of California, San Francisco, San Francisco, California, USA
| | - Shubir Dutt
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
- Department of Psychology, University of Southern California, Los Angeles, California, USA
| | - Mara Mather
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
- Department of Psychology, University of Southern California, Los Angeles, California, USA
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA
| | - Mareike Ludwig
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences, University of Magdeburg, Magdeburg, Germany
| | - Matthew J Betts
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences, University of Magdeburg, Magdeburg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
| | - Joseph R Winer
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Stefan Teipel
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Rostock/Greifswald, Rostock, Germany
- Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
| | - Alexandra J Weigand
- San Diego State University/University of California San Diego Joint Doctoral Program in Clinical Psychology, San Diego, California, USA
| | - Oxana Eschenko
- Department of Computational Neuroscience, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
| | - Dorothea Hämmerer
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
- Department of Psychology, University of Innsbruck, Innsbruck, Austria
- Institute of Cognitive Neuroscience, University College London, London, UK
| | - Marina Leiman
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
| | - Scott E Counts
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, Michigan, USA
- Department of Family Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Michigan Alzheimer's Disease Research Center, Ann Arbor, Michigan, USA
| | - James M Shine
- Brain and Mind Center, The University of Sydney, Sydney, Australia
| | - Ian H Robertson
- Global Brain Health Institute, Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
- Goizueta Institute, Emory University, Atlanta, Georgia, USA
| | - Elisa Lancini
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
| | - Gowoon Son
- Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Christoph Schneider
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maxime Van Egroo
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Faculty of Health, Medicine, and Life Sciences, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, the Netherlands
| | - Claudio Liguori
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Neurology Unit, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Qin Wang
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Agusta University, Agusta, Georgia, USA
| | - Elena M Vazey
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | | | - Lena Haag
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
| | - Mark W Bondi
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
- Psychology Service, VA San Diego Healthcare System, San Diego, California, USA
| | - Sven Vanneste
- Global Brain Health Institute, Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
- School of Psychology, Trinity College Dublin, Dublin, Ireland
- Trinity College Institute for Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Whitney M Freeze
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neuropsychology and Psychiatry, Maastricht University, Maastricht, the Netherlands
| | - Yeo-Jin Yi
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University, Magdeburg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
| | - Mihovil Maldinov
- Department of Psychiatry and Psychotherapy, University of Rostock, Rostock, Germany
| | - Jennifer Gatchel
- Division of Geriatric Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Abhijit Satpati
- Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Claudio Babiloni
- Department of Physiology and Pharmacology "V. Erspamer,", Sapienza University of Rome, Rome, Italy
- Hospital San Raffaele Cassino, Cassino, Italy
| | - William S Kremen
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, California, USA
| | - Robert Howard
- Division of Psychiatry, University College London, London, UK
| | - Heidi I L Jacobs
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Faculty of Health, Medicine, and Life Sciences, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, the Netherlands
| | - Lea T Grinberg
- Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
- Global Brain Health Institute, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of São Paulo Medical School, São Paulo, Brazil
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10
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Tan H, Hubertus S, Thomas S, Lee AM, Gerhardt S, Gerchen MF, Sommer WH, Kiefer F, Schad L, Vollstädt-Klein S. Association between iron accumulation in the dorsal striatum and compulsive drinking in alcohol use disorder. Psychopharmacology (Berl) 2023; 240:249-257. [PMID: 36577866 PMCID: PMC9879829 DOI: 10.1007/s00213-022-06301-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022]
Abstract
RATIONALE Brain iron accumulation has been observed in neuropsychiatric disorders and shown to be related to neurodegeneration. OBJECTIVES In this study, we used quantitative susceptibility mapping (QSM), an emerging MRI technique developed for quantifying tissue magnetic susceptibility, to examine brain iron accumulation in individuals with alcohol use disorder (AUD) and its relation to compulsive drinking. METHODS Based on our previous projects, QSM was performed as a secondary analysis with gradient echo sequence images, in 186 individuals with AUD and 274 healthy participants. Whole-brain susceptibility values were calculated with morphology-enabled dipole inversion and referenced to the cerebrospinal fluid. Then, the susceptibility maps were compared between AUD individuals and healthy participants. The relationship between drinking patterns and susceptibility was explored. RESULTS Whole-brain analyses showed that the susceptibility in the dorsal striatum (putamen and caudate) among AUD individuals was higher than healthy participants and was positively related to the Obsessive Compulsive Drinking Scale (OCDS) scores and the amount of drinking in the past three months. CONCLUSIONS Increased susceptibility suggests higher iron accumulation in the dorsal striatum in AUD. This surrogate for the brain iron level was linearly associated with the compulsive drinking pattern and the recent amount of drinking, which provides us a new clinical perspective in relation to brain iron accumulation, and also might indicate an association of AUD with neuroinflammation as a consequence of brain iron accumulation. The iron accumulation in the striatum is further relevant for functional imaging studies in AUD by potentially producing signal dropout and artefacts in fMRI images.
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Affiliation(s)
- Haoye Tan
- grid.7700.00000 0001 2190 4373Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Simon Hubertus
- grid.7700.00000 0001 2190 4373Computer Assisted Clinical Medicine, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Sebastian Thomas
- grid.7700.00000 0001 2190 4373Computer Assisted Clinical Medicine, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Alycia M. Lee
- grid.7700.00000 0001 2190 4373Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Sarah Gerhardt
- grid.7700.00000 0001 2190 4373Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Martin Fungisai Gerchen
- grid.7700.00000 0001 2190 4373Department of Clinical Psychology, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany ,grid.455092.fBernstein Center for Computational Neuroscience Heidelberg/Mannheim, 68159 Mannheim, Germany ,grid.7700.00000 0001 2190 4373Department of Psychology, Heidelberg University, 69117 Heidelberg, Germany
| | - Wolfgang H. Sommer
- grid.7700.00000 0001 2190 4373Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany ,grid.7700.00000 0001 2190 4373Institute of Psychopharmacology, Central Institute of Mental Health, Heidelberg University, 68159 Mannheim, Germany ,Bethania Hospital for Psychiatry, Psychosomatics, and Psychotherapy, Greifswald, Germany
| | - Falk Kiefer
- grid.7700.00000 0001 2190 4373Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany ,grid.7700.00000 0001 2190 4373Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany ,grid.7700.00000 0001 2190 4373Feuerlein Center on Translational Addiction Medicine, Heidelberg University, 69117 Heidelberg, Germany
| | - Lothar Schad
- grid.7700.00000 0001 2190 4373Computer Assisted Clinical Medicine, Medical Faculty of Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Sabine Vollstädt-Klein
- Department of Addictive Behaviour and Addiction Medicine, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, 68159, Mannheim, Germany. .,Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty of Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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11
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Fazal Z, Gomez DEP, Llera A, Marques JPRF, Beck T, Poser BA, Norris DG. A comparison of multiband and multiband multiecho gradient-echo EPI for task fMRI at 3 T. Hum Brain Mapp 2022; 44:82-93. [PMID: 36196782 PMCID: PMC9783458 DOI: 10.1002/hbm.26081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 02/05/2023] Open
Abstract
A multiband (MB) echo-planar imaging (EPI) sequence is compared to a multiband multiecho (MBME) EPI protocol to investigate differences in sensitivity for task functional magnetic resonance imaging (fMRI) at 3 T. Multiecho sampling improves sensitivity in areas where single-echo-EPI suffers from dropouts. However, It requires in-plane acceleration to reduce the echo train length, limiting the slice acceleration factor and the temporal and spatial resolution Data were acquired for both protocols in two sessions 24 h apart using an adapted color-word interference Stroop task. Besides protocol comparison statistically, we performed test-retest reliability across sessions for different protocols and denoising methods. We evaluated the sensitivity of two different echo-combination strategies for MBME-EPI. We examined the performance of three different data denoising approaches: "Standard," "AROMA," and "FIX" for MB and MBME, and assessed whether a specific method is preferable. We consider using an appropriate autoregressive model order within the general linear model framework to correct TR differences between the protocols. The comparison between protocols and denoising methods showed at group level significantly higher mean z-scores and the number of active voxels for MBME in the motor, subcortical and medial frontal cortices. When comparing different echo combinations, our results suggest that a contrast-to-noise ratio weighted echo combination improves sensitivity in MBME compared to simple echo-summation. This study indicates that MBME can be a preferred protocol in task fMRI at spatial resolution (≥2 mm), primarily in medial prefrontal and subcortical areas.
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Affiliation(s)
- Zahra Fazal
- Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Cognitive NeuroimagingRadboud University NijmegenNijmegenThe Netherlands
| | - Daniel E. P. Gomez
- Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Cognitive NeuroimagingRadboud University NijmegenNijmegenThe Netherlands
- Athinoula A. Martinos Center for Biomedical ImagingMassachusetts General HospitalBostonMassachusettsUSA
- Present address:
Department of Biomedical EngineeringBoston UniversityBostonMassachusettsUSA
| | - Alberto Llera
- Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Cognitive NeuroimagingRadboud University NijmegenNijmegenThe Netherlands
| | - José P. R. F. Marques
- Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Cognitive NeuroimagingRadboud University NijmegenNijmegenThe Netherlands
| | | | - Benedikt A. Poser
- Faculty of Psychology and NeuroscienceMaastricht UniversityMaastrichtNetherlands
| | - David G. Norris
- Donders Institute for Brain, Cognition and Behaviour, Donders Centre for Cognitive NeuroimagingRadboud University NijmegenNijmegenThe Netherlands
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, UNESCO‐Weltkulturerbe Zollverein, Leitstand Kokerei ZollvereinEssenGermany
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12
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Gu L, Shu H, Xu H, Wang Y. Functional brain changes in Parkinson’s disease: a whole brain ALE study. Neurol Sci 2022; 43:5909-5916. [DOI: 10.1007/s10072-022-06272-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/03/2022] [Indexed: 11/27/2022]
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13
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Kung PH, Soriano-Mas C, Steward T. The influence of the subcortex and brain stem on overeating: How advances in functional neuroimaging can be applied to expand neurobiological models to beyond the cortex. Rev Endocr Metab Disord 2022; 23:719-731. [PMID: 35380355 PMCID: PMC9307542 DOI: 10.1007/s11154-022-09720-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/13/2022]
Abstract
Functional neuroimaging has become a widely used tool in obesity and eating disorder research to explore the alterations in neurobiology that underlie overeating and binge eating behaviors. Current and traditional neurobiological models underscore the importance of impairments in brain systems supporting reward, cognitive control, attention, and emotion regulation as primary drivers for overeating. Due to the technical limitations of standard field strength functional magnetic resonance imaging (fMRI) scanners, human neuroimaging research to date has focused largely on cortical and basal ganglia effects on appetitive behaviors. The present review draws on animal and human research to highlight how neural signaling encoding energy regulation, reward-learning, and habit formation converge on hypothalamic, brainstem, thalamic, and striatal regions to contribute to overeating in humans. We also consider the role of regions such as the mediodorsal thalamus, ventral striatum, lateral hypothalamus and locus coeruleus in supporting habit formation, inhibitory control of food craving, and attentional biases. Through these discussions, we present proposals on how the neurobiology underlying these processes could be examined using functional neuroimaging and highlight how ultra-high field 7-Tesla (7 T) fMRI may be leveraged to elucidate the potential functional alterations in subcortical networks. Focus is given to how interactions of these regions with peripheral endocannabinoids and neuropeptides, such as orexin, could be explored. Technical and methodological aspects regarding the use of ultra-high field 7 T fMRI to study eating behaviors are also reviewed.
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Affiliation(s)
- Po-Han Kung
- Melbourne School of Psychological Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Victoria, Australia
| | - Carles Soriano-Mas
- Psychiatry and Mental Health Group, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Neuroscience Program, L'Hospitalet de Llobregat, Spain
- CIBERSAM, Carlos III Health Institute, Madrid, Spain
- Department of Social Psychology and Quantitative Psychology, University of Barcelona, Barcelona, Spain
| | - Trevor Steward
- Melbourne School of Psychological Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia.
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Victoria, Australia.
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14
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Liu TT, Li B, Fernandez B, Banerjee S. A Geometric View of Signal Sensitivity Metrics in multi-echo fMRI. Neuroimage 2022; 259:119409. [PMID: 35752411 DOI: 10.1016/j.neuroimage.2022.119409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/21/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
In multi-echo fMRI (ME-fMRI), two metrics have been widely used to measure the performance of various acquisition and analysis approaches. These are temporal SNR (tSNR) and differential contrast-to-noise ratio (dCNR). A key step in ME-fMRI is the weighted combination of the data from multiple echoes, and prior work has examined the dependence of tSNR and dCNR on the choice of weights. However, most studies have focused on only one of these two metrics, and the relationship between the two metrics has not been examined. In this work, we present a geometric view that offers greater insight into the relation between the two metrics and their weight dependence. We identify three major regimes: (1) a tSNR robust regime in which tSNR is robust to the weight selection with most weight variants achieving close to optimal performance, whereas dCNR shows a pronounced dependence on the weights with most variants achieving suboptimal performance; (2) a dCNR robust regime in which dCNR is robust to the weight selection with most weight variants achieving close to optimal performance, while tSNR exhibits a strong dependence on the weights with most variants achieving significantly lower than optimal performance; and (3) a within-type robust regime in which both tSNR and dCNR achieve nearly optimal performance when the form of the weights are variants of their respective optimal weights and exhibit a moderate decrease in performance for other weight variants. Insight into the behavior observed in the different regimes is gained by considering spherical representations of the weight dependence of the components used to form each metric. For multi-echo acquisitions, dCNR is shown to be more directly related than tSNR to measures of CNR and signal-to-noise ratio (SNR) for both task-based and resting-state fMRI scans, respectively.
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Affiliation(s)
- Thomas T Liu
- Center for Functional MRI, University of California San Diego, 9500 Gilman Drive MC 0677, La Jolla CA 92093, USA; Departments of Radiology, Psychiatry, and Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA.
| | - Bochao Li
- Department of Biomedical Engineering, University of Southern California, Los Angeles CA, USA
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15
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Okada T, Fujimoto K, Fushimi Y, Akasaka T, Thuy DHD, Shima A, Sawamoto N, Oishi N, Zhang Z, Funaki T, Nakamoto Y, Murai T, Miyamoto S, Takahashi R, Isa T. Neuroimaging at 7 Tesla: a pictorial narrative review. Quant Imaging Med Surg 2022; 12:3406-3435. [PMID: 35655840 PMCID: PMC9131333 DOI: 10.21037/qims-21-969] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/05/2022] [Indexed: 01/26/2024]
Abstract
Neuroimaging using the 7-Tesla (7T) human magnetic resonance (MR) system is rapidly gaining popularity after being approved for clinical use in the European Union and the USA. This trend is the same for functional MR imaging (MRI). The primary advantages of 7T over lower magnetic fields are its higher signal-to-noise and contrast-to-noise ratios, which provide high-resolution acquisitions and better contrast, making it easier to detect lesions and structural changes in brain disorders. Another advantage is the capability to measure a greater number of neurochemicals by virtue of the increased spectral resolution. Many structural and functional studies using 7T have been conducted to visualize details in the white matter and layers of the cortex and hippocampus, the subnucleus or regions of the putamen, the globus pallidus, thalamus and substantia nigra, and in small structures, such as the subthalamic nucleus, habenula, perforating arteries, and the perivascular space, that are difficult to observe at lower magnetic field strengths. The target disorders for 7T neuroimaging range from tumoral diseases to vascular, neurodegenerative, and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy, major depressive disorder, and schizophrenia. MR spectroscopy has also been used for research because of its increased chemical shift that separates overlapping peaks and resolves neurochemicals more effectively at 7T than a lower magnetic field. This paper presents a narrative review of these topics and an illustrative presentation of images obtained at 7T. We expect 7T neuroimaging to provide a new imaging biomarker of various brain disorders.
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Affiliation(s)
- Tomohisa Okada
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Fujimoto
- Department of Real World Data Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasutaka Fushimi
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thai Akasaka
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Dinh H. D. Thuy
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Shima
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobukatsu Sawamoto
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoya Oishi
- Medial Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Zhilin Zhang
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Funaki
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuji Nakamoto
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Susumu Miyamoto
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Isa
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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16
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Pilmeyer J, Huijbers W, Lamerichs R, Jansen JFA, Breeuwer M, Zinger S. Functional MRI in major depressive disorder: A review of findings, limitations, and future prospects. J Neuroimaging 2022; 32:582-595. [PMID: 35598083 PMCID: PMC9540243 DOI: 10.1111/jon.13011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 02/02/2023] Open
Abstract
Objective diagnosis and prognosis in major depressive disorder (MDD) remains a challenge due to the absence of biomarkers based on physiological parameters or medical tests. Numerous studies have been conducted to identify functional magnetic resonance imaging‐based biomarkers of depression that either objectively differentiate patients with depression from healthy subjects, predict personalized treatment outcome, or characterize biological subtypes of depression. While there are some findings of consistent functional biomarkers, there is still lack of robust data acquisition and analysis methodology. According to current findings, primarily, the anterior cingulate cortex, prefrontal cortex, and default mode network play a crucial role in MDD. Yet, there are also less consistent results and the involvement of other regions or networks remains ambiguous. We further discuss image acquisition, processing, and analysis limitations that might underlie these inconsistencies. Finally, the current review aims to address and discuss possible remedies and future opportunities that could improve the search for consistent functional imaging biomarkers of depression. Novel acquisition techniques, such as multiband and multiecho imaging, and neural network‐based cleaning approaches can enhance the signal quality in limbic and frontal regions. More comprehensive analyses, such as directed or dynamic functional features or the identification of biological depression subtypes, can improve objective diagnosis or treatment outcome prediction and mitigate the heterogeneity of MDD. Overall, these improvements in functional MRI imaging techniques, processing, and analysis could advance the search for biomarkers and ultimately aid patients with MDD and their treatment course.
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Affiliation(s)
- Jesper Pilmeyer
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Research and Development, Epilepsy Centre Kempenhaeghe, Heeze, The Netherlands
| | - Willem Huijbers
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Philips Research, Eindhoven, The Netherlands
| | - Rolf Lamerichs
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Research and Development, Epilepsy Centre Kempenhaeghe, Heeze, The Netherlands.,Philips Research, Eindhoven, The Netherlands
| | - Jacobus F A Jansen
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands.,School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Marcel Breeuwer
- Philips Healthcare, Best, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Svitlana Zinger
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Research and Development, Epilepsy Centre Kempenhaeghe, Heeze, The Netherlands
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17
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Kovářová A, Gajdoš M, Rektor I, Mikl M. Contribution of the multi-echo approach in accelerated functional magnetic resonance imaging multiband acquisition. Hum Brain Mapp 2021; 43:955-973. [PMID: 34716738 PMCID: PMC8764472 DOI: 10.1002/hbm.25698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/16/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022] Open
Abstract
We wanted to verify the effect of combining multi‐echo (ME) functional magnetic resonance imaging (fMRI) with slice acceleration in simultaneous multi‐slice acquisition. The aim was to shed light on the benefits of multiple echoes for various acquisition settings, especially for levels of slice acceleration and flip angle. Whole‐brain ME fMRI data were obtained from 26 healthy volunteers (using three echoes; seven runs with slice acceleration 1, 4, 6, and 8; and two different flip angles for each of the first three acceleration factors) and processed as single‐echo (SE) data and ME data based on optimal combinations weighted by the contrast‐to‐noise ratio. Global metrics (temporal signal‐to‐noise ratio, signal‐to‐noise separation, number of active voxels, etc.) and local characteristics in regions of interest were used to evaluate SE and ME data. ME results outperformed SE results in all runs; the differences became more apparent for higher acceleration, where a significant decrease in data quality is observed. ME fMRI can improve the observed data quality metrics over SE fMRI for a wide range of accelerated fMRI acquisitions.
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Affiliation(s)
- Anežka Kovářová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,First Department of Neurology, Faculty of Medicine of the Masaryk University, Brno, Czech Republic
| | - Martin Gajdoš
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ivan Rektor
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,First Department of Neurology, Faculty of Medicine of the Masaryk University, Brno, Czech Republic
| | - Michal Mikl
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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18
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Cohen AD, Jagra AS, Yang B, Fernandez B, Banerjee S, Wang Y. Detecting Task Functional MRI Activation Using the Multiband Multiecho (MBME) Echo-Planar Imaging (EPI) Sequence. J Magn Reson Imaging 2021; 53:1366-1374. [PMID: 33210793 PMCID: PMC10937038 DOI: 10.1002/jmri.27448] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Blood oxygen level-dependent (BOLD) functional MRI (fMRI) has been widely applied to detect brain activations. Recent advances in multiband (MB) and multiecho (ME) techniques have greatly improved fMRI methods. MB imaging improves temporal and/or spatial resolution, while ME imaging has been shown to improve BOLD sensitivity. This study aimed to evaluate the novel MBME echo planar imaging (EPI) sequence utilizing MB and ME simultaneously to determine if the MBME outperform the MB single echo (MBSE) sequence for task fMRI. PURPOSE To compare the performance of MBME with MBSE in a task fMRI study. STUDY TYPE Prospective. POPULATION A total of 29 healthy volunteers aged 20-46 years (9 male, 20 female). FIELD STRENGTH/SEQUENCE MBSE and MBME gradient-echo EPI sequences were applied at 3T. Additional T1 -weighted magnetization-prepared rapid acquisition with gradient echo (MPRAGE) was collected. ASSESSMENT A checkerboard visual task was presented during the functional MBSE and MBME scans. The MBME or MBSE signal was evaluated using the temporal signal-to-noise ratio (tSNR). Task activation was evaluated using the z-score, volume, sensitivity, and specificity. Test-retest metrics of task activation were examined with the Dice coefficient (DC) and intraclass correlation coefficient (ICC) on subjects with repeated scans. STATISTICAL TESTS A linear mixed-effects model was used to compared MBME and MBSE activation at the voxel base. The paired t-test was used to compare tSNR, activation z-score, and volume, along with sensitivity, specificity, and DC between MBSE and MBME. RESULTS While similar task activation was detected in the visual cortex, MBME showed higher activation volume and higher sensitivity compared with MBSE (P < 0.05). ICC was higher for MBME than MBSE, while there was a trend of differences in DC (P = 0.08). DATA CONCLUSION MBME resulted in higher task fMRI activation volume and sensitivity without losing specificity. Reliability was also higher for MBME scans compared with MBSE. LEVEL OF EVIDENCE 1 TECHNICAL EFFICACY STAGE: 1.
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Affiliation(s)
- Alexander D. Cohen
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | | | | | | | | | - Yang Wang
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, United States
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19
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Ngo GN, Haak KV, Beckmann CF, Menon RS. Mesoscale hierarchical organization of primary somatosensory cortex captured by resting-state-fMRI in humans. Neuroimage 2021; 235:118031. [PMID: 33836270 DOI: 10.1016/j.neuroimage.2021.118031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 12/25/2022] Open
Abstract
The primary somatosensory cortex (S1) plays a key role in the processing and integration of afferent somatosensory inputs along an anterior-to-posterior axis, contributing towards necessary human function. It is believed that anatomical connectivity can be used to probe hierarchical organization, however direct characterization of this principle in-vivo within humans remains elusive. Here, we use resting-state functional connectivity as a complement to anatomical connectivity to investigate topographical principles of human S1. We employ a novel approach to examine mesoscopic variations of functional connectivity, and demonstrate a topographic organisation spanning the region's hierarchical axis that strongly correlates with underlying microstructure while tracing along architectonic Brodmann areas. Our findings characterize anatomical hierarchy of S1 as a 'continuous spectrum' with evidence supporting a functional boundary between areas 3b and 1. The identification of this topography bridges the gap between structure and connectivity, and may be used to help further current understanding of sensorimotor deficits.
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Affiliation(s)
- Geoffrey N Ngo
- Department of Medical Biophysics, University of Western Ontario, London, Ontario, Canada
| | - Koen V Haak
- Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Christian F Beckmann
- Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford OX3 9DU, UK
| | - Ravi S Menon
- Department of Medical Biophysics, University of Western Ontario, London, Ontario, Canada; Centre for Functional and Metabolic Mapping, Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.
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20
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Moia S, Termenon M, Uruñuela E, Chen G, Stickland RC, Bright MG, Caballero-Gaudes C. ICA-based denoising strategies in breath-hold induced cerebrovascular reactivity mapping with multi echo BOLD fMRI. Neuroimage 2021; 233:117914. [PMID: 33684602 PMCID: PMC8351526 DOI: 10.1016/j.neuroimage.2021.117914] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/25/2021] [Accepted: 02/22/2021] [Indexed: 12/19/2022] Open
Abstract
Performing a BOLD functional MRI (fMRI) acquisition during breath-hold (BH) tasks is a non-invasive, robust method to estimate cerebrovascular reactivity (CVR). However, movement and breathing-related artefacts caused by the BH can substantially hinder CVR estimates due to their high temporal collinearity with the effect of interest, and attention has to be paid when choosing which analysis model should be applied to the data. In this study, we evaluate the performance of multiple analysis strategies based on lagged general linear models applied on multi-echo BOLD fMRI data, acquired in ten subjects performing a BH task during ten sessions, to obtain subject-specific CVR and haemodynamic lag estimates. The evaluated approaches range from conventional regression models, i.e. including drifts and motion timecourses as nuisance regressors, applied on single-echo or optimally-combined data, to more complex models including regressors obtained from multi-echo independent component analysis with different grades of orthogonalization in order to preserve the effect of interest, i.e. the CVR. We compare these models in terms of their ability to make signal intensity changes independent from motion, as well as the reliability as measured by voxelwise intraclass correlation coefficients of both CVR and lag maps over time. Our results reveal that a conservative independent component analysis model applied on the optimally-combined multi-echo fMRI signal offers the largest reduction of motion-related effects in the signal, while yielding reliable CVR amplitude and lag estimates, although a conventional regression model applied on the optimally-combined data results in similar estimates. This work demonstrates the usefulness of multi-echo based fMRI acquisitions and independent component analysis denoising for precision mapping of CVR in single subjects based on BH paradigms, fostering its potential as a clinically-viable neuroimaging tool for individual patients. It also proves that the way in which data-driven regressors should be incorporated in the analysis model is not straight-forward due to their complex interaction with the BH-induced BOLD response.
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Affiliation(s)
- Stefano Moia
- Basque Center on Cognition, Brain and Language, Donostia, Spain; University of the Basque Country UPV/EHU, Donostia, Spain.
| | - Maite Termenon
- Basque Center on Cognition, Brain and Language, Donostia, Spain
| | - Eneko Uruñuela
- Basque Center on Cognition, Brain and Language, Donostia, Spain; University of the Basque Country UPV/EHU, Donostia, Spain
| | - Gang Chen
- Scientific and Statistical Computing Core, NIMH/NIH/HHS, Bethesda, MD, United States
| | - Rachael C Stickland
- Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Molly G Bright
- Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States; Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, United States
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21
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Cash RFH, Cocchi L, Lv J, Wu Y, Fitzgerald PB, Zalesky A. Personalized connectivity-guided DLPFC-TMS for depression: Advancing computational feasibility, precision and reproducibility. Hum Brain Mapp 2021; 42:4155-4172. [PMID: 33544411 PMCID: PMC8357003 DOI: 10.1002/hbm.25330] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/16/2020] [Accepted: 12/13/2020] [Indexed: 01/18/2023] Open
Abstract
Repetitive transcranial magnetic stimulation (rTMS) of the dorsolateral prefrontal cortex (DLPFC) is an established treatment for refractory depression, however, therapeutic outcomes vary. Mounting evidence suggests that clinical response relates to functional connectivity with the subgenual cingulate cortex (SGC) at the precise DLPFC stimulation site. Critically, SGC-related network architecture shows considerable interindividual variation across the spatial extent of the DLPFC, indicating that connectivity-based target personalization could potentially be necessary to improve treatment outcomes. However, to date accurate personalization has not appeared feasible, with recent work indicating that the intraindividual reproducibility of optimal targets is limited to 3.5 cm. Here we developed reliable and accurate methodologies to compute individualized connectivity-guided stimulation targets. In resting-state functional MRI scans acquired across 1,000 healthy adults, we demonstrate that, using this approach, personalized targets can be reliably and robustly pinpointed, with a median accuracy of ~2 mm between scans repeated across separate days. These targets remained highly stable, even after 1 year, with a median intraindividual distance between coordinates of only 2.7 mm. Interindividual spatial variation in personalized targets exceeded intraindividual variation by a factor of up to 6.85, suggesting that personalized targets did not trivially converge to a group-average site. Moreover, personalized targets were heritable, suggesting that connectivity-guided rTMS personalization is stable over time and under genetic control. This computational framework provides capacity for personalized connectivity-guided TMS targets to be robustly computed with high precision and has the flexibly to advance research in other basic research and clinical applications.
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Affiliation(s)
- Robin F H Cash
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia
| | - Luca Cocchi
- Clinical Brain Networks Group, QIMR Berghofer, Brisbane, Queensland, Australia
| | - Jinglei Lv
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia.,School of Biomedical Engineering, The University of Sydney, Camperdown, New South Wales, Australia
| | - Yumeng Wu
- Department of Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul B Fitzgerald
- Epworth Centre for Innovation and Mental Health, Epworth Healthcare and the Monash University Central Clinical School, Camberwell, Victoria, Australia
| | - Andrew Zalesky
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia
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22
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Miletić S, Bazin PL, Weiskopf N, van der Zwaag W, Forstmann BU, Trampel R. fMRI protocol optimization for simultaneously studying small subcortical and cortical areas at 7 T. Neuroimage 2020; 219:116992. [DOI: 10.1016/j.neuroimage.2020.116992] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
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23
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Tian Y, Margulies DS, Breakspear M, Zalesky A. Topographic organization of the human subcortex unveiled with functional connectivity gradients. Nat Neurosci 2020; 23:1421-1432. [PMID: 32989295 DOI: 10.1038/s41593-020-00711-6] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
Brain atlases are fundamental to understanding the topographic organization of the human brain, yet many contemporary human atlases cover only the cerebral cortex, leaving the subcortex a terra incognita. We use functional MRI (fMRI) to map the complex topographic organization of the human subcortex, revealing large-scale connectivity gradients and new areal boundaries. We unveil four scales of subcortical organization that recapitulate well-known anatomical nuclei at the coarsest scale and delineate 27 new bilateral regions at the finest. Ultrahigh field strength fMRI corroborates and extends this organizational structure, enabling the delineation of finer subdivisions of the hippocampus and the amygdala, while task-evoked fMRI reveals a subtle subcortical reorganization in response to changing cognitive demands. A new subcortical atlas is delineated, personalized to represent individual differences and used to uncover reproducible brain-behavior relationships. Linking cortical networks to subcortical regions recapitulates a task-positive to task-negative axis. This new atlas enables holistic connectome mapping and characterization of cortico-subcortical connectivity.
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Affiliation(s)
- Ye Tian
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia.
| | - Daniel S Margulies
- Centre National de la Recherche Scientifique (CNRS) UMR 8002, Integrative Neuroscience and Cognition Center, Université de Paris, Paris, France
| | - Michael Breakspear
- Discipline of Psychiatry, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,School of Psychology, Faculty of Science, University of Newcastle, Newcastle, New South Wales, Australia
| | - Andrew Zalesky
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia. .,Department of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, Victoria, Australia.
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24
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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: 4.6] [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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25
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Siemonsma S, Kruger S, Balachandrasekaran A, Mani M, Jacob M. MULTI-ECHO RECOVERY WITH FIELD INHOMOGENEITY COMPENSATION USING STRUCTURED LOW-RANK MATRIX COMPLETION. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2020; 2020:1074-1077. [PMID: 34671437 PMCID: PMC8526283 DOI: 10.1109/isbi45749.2020.9098418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Echo-planar imaging (EPI), which is the main workhorse of functional MRI, suffers from field inhomogeneity-induced geometric distortions. The amount of distortion is proportional to the readout duration, which restricts the maximum achievable spatial resolution. The spatially varying nature of the T 2 * decay makes it challenging for EPI schemes with a single echo time to obtain good sensitivity to functional activations in different brain regions. Despite the use of parallel MRI and multislice acceleration, the number of different echo times that can be acquired in a reasonable TR is limited. The main focus of this work is to introduce a rosette-based acquisition scheme and a structured low-rank reconstruction algorithm to overcome the above challenges. The proposed scheme exploits the exponential structure of the time series to recover distortion-free images from several echoes simultaneously.
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26
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Caballero-Gaudes C, Moia S, Panwar P, Bandettini PA, Gonzalez-Castillo J. A deconvolution algorithm for multi-echo functional MRI: Multi-echo Sparse Paradigm Free Mapping. Neuroimage 2019; 202:116081. [PMID: 31419613 DOI: 10.1016/j.neuroimage.2019.116081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/01/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022] Open
Abstract
This work introduces a novel algorithm for deconvolution of the BOLD signal in multi-echo fMRI data: Multi-echo Sparse Paradigm Free Mapping (ME-SPFM). Assuming a linear dependence of the BOLD percent signal change on the echo time (TE) and using sparsity-promoting regularized least squares estimation, ME-SPFM yields voxelwise time-varying estimates of the changes in the apparent transverse relaxation (ΔR2⁎) without prior knowledge of the timings of individual BOLD events. Our results in multi-echo fMRI data collected during a multi-task event-related paradigm at 3 Tesla demonstrate that the maps of R2⁎ changes obtained with ME-SPFM at the times of the stimulus trials show high spatial and temporal concordance with the activation maps and BOLD signals obtained with standard model-based analysis. This method yields estimates of ΔR2⁎ having physiologically plausible values. Owing to its ability to blindly detect events, ME-SPFM also enables us to map ΔR2⁎ associated with spontaneous, transient BOLD responses occurring between trials. This framework is a step towards deciphering the dynamic nature of brain activity in naturalistic paradigms, resting-state or experimental paradigms with unknown timing of the BOLD events.
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Affiliation(s)
| | - Stefano Moia
- Basque Center on Cognition, Brain and Language, San Sebastian, Spain
| | - Puja Panwar
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA
| | - Peter A Bandettini
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA; Functional MRI Core, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA
| | - Javier Gonzalez-Castillo
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA
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27
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Torrisi S, Chen G, Glen D, Bandettini PA, Baker CI, Reynolds R, Yen-Ting Liu J, Leshin J, Balderston N, Grillon C, Ernst M. Statistical power comparisons at 3T and 7T with a GO / NOGO task. Neuroimage 2018; 175:100-110. [PMID: 29621615 DOI: 10.1016/j.neuroimage.2018.03.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/13/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022] Open
Abstract
The field of cognitive neuroscience is weighing evidence about whether to move from standard field strength to ultra-high field (UHF). The present study contributes to the evidence by comparing a cognitive neuroscience paradigm at 3 Tesla (3T) and 7 Tesla (7T). The goal was to test and demonstrate the practical effects of field strength on a standard GO/NOGO task using accessible preprocessing and analysis tools. Two independent matched healthy samples (N = 31 each) were analyzed at 3T and 7T. Results show gains at 7T in statistical strength, the detection of smaller effects and group-level power. With an increased availability of UHF scanners, these gains may be exploited by cognitive neuroscientists and other neuroimaging researchers to develop more efficient or comprehensive experimental designs and, given the same sample size, achieve greater statistical power at 7T.
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Affiliation(s)
- Salvatore Torrisi
- Section on Neurobiology of Fear and Anxiety, NIMH, Bethesda MD, United States.
| | - Gang Chen
- Scientific and Statistical Computing Core, NIMH, Bethesda MD, United States
| | - Daniel Glen
- Scientific and Statistical Computing Core, NIMH, Bethesda MD, United States
| | | | - Chris I Baker
- Section on Learning and Plasticity, NIMH, Bethesda MD, United States
| | - Richard Reynolds
- Scientific and Statistical Computing Core, NIMH, Bethesda MD, United States
| | | | - Joseph Leshin
- Section on Neurobiology of Fear and Anxiety, NIMH, Bethesda MD, United States
| | - Nicholas Balderston
- Section on Neurobiology of Fear and Anxiety, NIMH, Bethesda MD, United States
| | - Christian Grillon
- Section on Neurobiology of Fear and Anxiety, NIMH, Bethesda MD, United States
| | - Monique Ernst
- Section on Neurobiology of Fear and Anxiety, NIMH, Bethesda MD, United States
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