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Shao R, Wang T, Hang C, An L, Wang X, Zhang L, Yu J, Shan Z, Yang Q, Tang Z. Alteration in early resting‑state functional MRI activity in comatose survivors of cardiac arrest: a prospective cohort study. Crit Care 2024; 28:260. [PMID: 39095884 PMCID: PMC11295486 DOI: 10.1186/s13054-024-05045-4] [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: 05/09/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND This study aimed to explore the characteristics of abnormal regional resting-state functional magnetic resonance imaging (rs-fMRI) activity in comatose patients in the early period after cardiac arrest (CA), and to investigate their relationships with neurological outcomes. We also explored the correlations between jugular venous oxygen saturation (SjvO2) and rs-fMRI activity in resuscitated comatose patients. We also examined the relationship between the amplitude of the N20-baseline and the rs-fMRI activity within the intracranial conduction pathway of somatosensory evoked potentials (SSEPs). METHODS Between January 2021 and January 2024, eligible post-resuscitated patients were screened to undergo fMRI examination. The amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), and regional homogeneity (ReHo) of rs-fMRI blood oxygenation level-dependent (BOLD) signals were used to characterize regional neural activity. Neurological outcomes were evaluated using the Glasgow-Pittsburgh cerebral performance category (CPC) scale at 3 months after CA. RESULTS In total, 20 healthy controls and 31 post-resuscitated patients were enrolled in this study. The rs-fMRI activity of resuscitated patients revealed complex changes, characterized by increased activity in some local brain regions and reduced activity in others compared to healthy controls (P < 0.05). However, the mean ALFF values of the whole brain were significantly greater in CA patients (P = 0.011). Among the clusters of abnormal rs-fMRI activity, the cluster values of ALFF in the left middle temporal gyrus and inferior temporal gyrus and the cluster values of ReHo in the right precentral gyrus, superior frontal gyrus and middle frontal gyrus were strongly correlated with the CPC score (P < 0.001). There was a strong correlation between the mean ALFF and SjvO2 in CA patients (r = 0.910, P < 0.001). The SSEP N20-baseline amplitudes in CA patients were negatively correlated with thalamic rs-fMRI activity (all P < 0.001). CONCLUSIONS This study revealed that abnormal rs-fMRI BOLD signals in resuscitated patients showed complex changes, characterized by increased activity in some local brain regions and reduced activity in others. Abnormal BOLD signals were associated with neurological outcomes in resuscitated patients. The mean ALFF values of the whole brain were closely related to SjvO2 levels, and changes in the thalamic BOLD signals correlated with the N20-baseline amplitudes of SSEP responses. TRIAL REGISTRATION NCT05966389 (Registered July 27, 2023).
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Affiliation(s)
- Rui Shao
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Tao Wang
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Chenchen Hang
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Le An
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Xingsheng Wang
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Luying Zhang
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Jingfei Yu
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Zhenyu Shan
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China
| | - Qi Yang
- Department of Radiology, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China.
| | - Ziren Tang
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, 8# Worker's Stadium South Road, Chao-yang District, Beijing, 100020, China.
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Reddy NA, Clements RG, Brooks JCW, Bright MG. Simultaneous cortical, subcortical, and brainstem mapping of sensory activation. Cereb Cortex 2024; 34:bhae273. [PMID: 38940832 PMCID: PMC11212354 DOI: 10.1093/cercor/bhae273] [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: 04/15/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
Nonpainful tactile sensory stimuli are processed in the cortex, subcortex, and brainstem. Recent functional magnetic resonance imaging studies have highlighted the value of whole-brain, systems-level investigation for examining sensory processing. However, whole-brain functional magnetic resonance imaging studies are uncommon, in part due to challenges with signal to noise when studying the brainstem. Furthermore, differentiation of small sensory brainstem structures such as the cuneate and gracile nuclei necessitates high-resolution imaging. To address this gap in systems-level sensory investigation, we employed a whole-brain, multi-echo functional magnetic resonance imaging acquisition at 3T with multi-echo independent component analysis denoising and brainstem-specific modeling to enable detection of activation across the entire sensory system. In healthy participants, we examined patterns of activity in response to nonpainful brushing of the right hand, left hand, and right foot (n = 10 per location), and found the expected lateralization, with distinct cortical and subcortical responses for upper and lower limb stimulation. At the brainstem level, we differentiated the adjacent cuneate and gracile nuclei, corresponding to hand and foot stimulation respectively. Our findings demonstrate that simultaneous cortical, subcortical, and brainstem mapping at 3T could be a key tool to understand the sensory system in both healthy individuals and clinical cohorts with sensory deficits.
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Affiliation(s)
- Neha A Reddy
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, United States
| | - Rebecca G Clements
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, United States
| | - Jonathan C W Brooks
- School of Psychology, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Molly G Bright
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, United States
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Zvolanek KM, Moore JE, Jarvis K, Moum SJ, Bright MG. Macrovascular blood flow and microvascular cerebrovascular reactivity are regionally coupled in adolescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.590312. [PMID: 38746187 PMCID: PMC11092525 DOI: 10.1101/2024.04.26.590312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cerebrovascular imaging assessments are particularly challenging in adolescent cohorts, where not all modalities are appropriate, and rapid brain maturation alters hemodynamics at both macro- and microvascular scales. In a preliminary sample of healthy adolescents (n=12, 8-25 years), we investigated relationships between 4D flow MRI-derived blood velocity and blood flow in bilateral anterior, middle, and posterior cerebral arteries and BOLD cerebrovascular reactivity in associated vascular territories. As hypothesized, higher velocities in large arteries are associated with an earlier response to a vasodilatory stimulus (cerebrovascular reactivity delay) in the downstream territory. Higher blood flow through these arteries is associated with a larger BOLD response to a vasodilatory stimulus (cerebrovascular reactivity amplitude) in the associated territory. These trends are consistent in a case study of adult moyamoya disease. In our small adolescent cohort, macrovascular-microvascular relationships for velocity/delay and flow/CVR change with age, though underlying mechanisms are unclear. Our work emphasizes the need to better characterize this key stage of human brain development, when cerebrovascular hemodynamics are changing, and standard imaging methods offer limited insight into these processes. We provide important normative data for future comparisons in pathology, where combining macro- and microvascular assessments may better help us prevent, stratify, and treat cerebrovascular disease.
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Reddy NA, Clements RG, Brooks JCW, Bright MG. Simultaneous cortical, subcortical, and brainstem mapping of sensory activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589099. [PMID: 38659741 PMCID: PMC11042175 DOI: 10.1101/2024.04.11.589099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Non-painful tactile sensory stimuli are processed in the cortex, subcortex, and brainstem. Recent functional magnetic resonance imaging (fMRI) studies have highlighted the value of whole-brain, systems-level investigation for examining pain processing. However, whole-brain fMRI studies are uncommon, in part due to challenges with signal to noise when studying the brainstem. Furthermore, the differentiation of small sensory brainstem structures such as the cuneate and gracile nuclei necessitates high resolution imaging. To address this gap in systems-level sensory investigation, we employed a whole-brain, multi-echo fMRI acquisition at 3T with multi-echo independent component analysis (ME-ICA) denoising and brainstem-specific modeling to enable detection of activation across the entire sensory system. In healthy participants, we examined patterns of activity in response to non-painful brushing of the right hand, left hand, and right foot, and found the expected lateralization, with distinct cortical and subcortical responses for upper and lower limb stimulation. At the brainstem level, we were able to differentiate the small, adjacent cuneate and gracile nuclei, corresponding to hand and foot stimulation respectively. Our findings demonstrate that simultaneous cortical, subcortical, and brainstem mapping at 3T could be a key tool to understand the sensory system in both healthy individuals and clinical cohorts with sensory deficits.
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Affiliation(s)
- Neha A. Reddy
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, United States
| | - Rebecca G. Clements
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, United States
| | | | - Molly G. Bright
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, United States
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Richerson WT, Meier TB, Cohen AD, Wang Y, Goodman MJ, Schmit BD, Wolfgram DF. Cerebrovascular Function is Altered in Hemodialysis Patients. KIDNEY360 2023; 4:1717-1725. [PMID: 37962988 PMCID: PMC10758518 DOI: 10.34067/kid.0000000000000292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023]
Abstract
Key Points Hemodialysis patients have impaired cerebrovascular reactivity. Hemodialysis patients have cerebral structural deficits. Background Hemodialysis patients have declines in cerebral blood flow (CBF) and cerebral oxygenation during hemodialysis that may lead to ischemic brain injury. Cerebrovascular reactivity (CVR) may indicate which individuals are more susceptible to intradialytic hypoperfusion and ischemia. We hypothesized that hemodialysis patients would have decreased CVR and increased CBF relative to controls and deficits in CVR would be related to brain structural deficits. Methods We measured cortical thickness and white matter hyperintensity (WMH) volume from T1 and T2 fluid attenuation inversion recovery images, respectively; CVR from a breath hold blood oxygen level–dependent CVR functional magnetic resonance imaging (fMRI); and arterial transit time and CBF from arterial spin labeling. Cerebrovascular and structural deficits in gray matter and white matter (GM and WM) were tested by averaging across the tissue and with a pothole analysis. Finally, we correlated cortical thickness and WMH volume with GM and WM cerebrovascular variables to assess the relationship between brain structure and cerebrovascular health. Results In ten hemodialysis patients, cortical thickness was found to be decreased (P = 0.002), WMH volume increased (P = 0.004), and WM CBF increased (P = 0.02) relative to ten controls. Pothole analysis indicated a higher number of increased GM and WM CBF voxels (P = 0.03, P = 0.02) and a higher number of decreased GM and WM CVR voxels (P = 0.02, P = 0.01). Conclusions This pilot study demonstrates that hemodialysis patients have decreased CVR and increased CBF relative to controls, along with reduced brain integrity. Further investigation is required to fully understand whether these cerebrovascular deficits may lead to structural changes.
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Affiliation(s)
- Wesley T. Richerson
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Timothy B. Meier
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Alexander D. Cohen
- Department of Radiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yang Wang
- Department of Radiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Brian D. Schmit
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Dawn F. Wolfgram
- Department of Medicine, Medical College of Wisconsin, Zablocki Veterans Affairs Medical Center, Milwaukee, Wisconsin
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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: 1] [Impact Index Per Article: 1.0] [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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Kang D, In MH, Jo HJ, Halverson MA, Meyer NK, Ahmed Z, Gray EM, Madhavan R, Foo TK, Fernandez B, Black DF, Welker KM, Trzasko JD, Huston J, Bernstein MA, Shu Y. Improved Resting-State Functional MRI Using Multi-Echo Echo-Planar Imaging on a Compact 3T MRI Scanner with High-Performance Gradients. SENSORS (BASEL, SWITZERLAND) 2023; 23:4329. [PMID: 37177534 PMCID: PMC10181561 DOI: 10.3390/s23094329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
In blood-oxygen-level-dependent (BOLD)-based resting-state functional (RS-fMRI) studies, usage of multi-echo echo-planar-imaging (ME-EPI) is limited due to unacceptable late echo times when high spatial resolution is used. Equipped with high-performance gradients, the compact 3T MRI system (C3T) enables a three-echo whole-brain ME-EPI protocol with smaller than 2.5 mm isotropic voxel and shorter than 1 s repetition time, as required in landmark fMRI studies. The performance of the ME-EPI was comprehensively evaluated with signal variance reduction and region-of-interest-, seed- and independent-component-analysis-based functional connectivity analyses and compared with a counterpart of single-echo EPI with the shortest TR possible. Through the multi-echo combination, the thermal noise level is reduced. Functional connectivity, as well as signal intensity, are recovered in the medial orbital sulcus and anterior transverse collateral sulcus in ME-EPI. It is demonstrated that ME-EPI provides superior sensitivity and accuracy for detecting functional connectivity and/or brain networks in comparison with single-echo EPI. In conclusion, the high-performance gradient enabled high-spatial-temporal resolution ME-EPI would be the method of choice for RS-fMRI study on the C3T.
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Affiliation(s)
- Daehun Kang
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Myung-Ho In
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Hang Joon Jo
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
- Department of Physiology, Hanyang University, Seoul 04763, Republic of Korea
| | | | - Nolan K. Meyer
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Zaki Ahmed
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Erin M. Gray
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | | | | | | | - David F. Black
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Kirk M. Welker
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Joshua D. Trzasko
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - John Huston
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Matt A. Bernstein
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
| | - Yunhong Shu
- Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA; (D.K.)
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Gong J, Stickland RC, Bright MG. Hemodynamic timing in resting-state and breathing-task BOLD fMRI. Neuroimage 2023; 274:120120. [PMID: 37072074 DOI: 10.1016/j.neuroimage.2023.120120] [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: 11/14/2022] [Revised: 04/06/2023] [Accepted: 04/15/2023] [Indexed: 04/20/2023] Open
Abstract
The blood flow response to a vasoactive stimulus demonstrates regional heterogeneity across both the healthy brain and in cerebrovascular pathology. The timing of a regional hemodynamic response is emerging as an important biomarker of cerebrovascular dysfunction, as well as a confound within fMRI analyses. Previous research demonstrated that hemodynamic timing is more robustly characterized when a larger systemic vascular response is evoked by a breathing challenge, compared to when only spontaneous fluctuations in vascular physiology are present (i.e., in resting-state data). However, it is not clear whether hemodynamic delays in these two conditions are physiologically interchangeable, and how methodological signal-to-noise factors may limit their agreement. To address this, we generated whole-brain maps of hemodynamic delays in nine healthy adults. We assessed the agreement of voxel-wise gray matter (GM) hemodynamic delays between two conditions: resting-state and breath-holding. We found that delay values demonstrated poor agreement when considering all GM voxels, but increasingly greater agreement when limiting analyses to voxels showing strong correlation with the GM mean time-series. Voxels showing the strongest agreement with the GM mean time-series were primarily located near large venous vessels, however these voxels explain some, but not all, of the observed agreement in timing. Increasing the degree of spatial smoothing of the fMRI data enhanced the correlation between individual voxel time-series and the GM mean time-series. These results suggest that signal-to-noise factors may be limiting the accuracy of voxel-wise timing estimates and hence their agreement between the two data segments. In conclusion, caution must be taken when using voxel-wise delay estimates from resting-state and breathing-task data interchangeably, and additional work is needed to evaluate their relative sensitivity and specificity to aspects of vascular physiology and pathology.
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Affiliation(s)
- Jingxuan Gong
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
| | - Rachael C Stickland
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Molly G Bright
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA; Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Zvolanek KM, Moia S, Dean JN, Stickland RC, Caballero-Gaudes C, Bright MG. Comparing end-tidal CO 2, respiration volume per time (RVT), and average gray matter signal for mapping cerebrovascular reactivity amplitude and delay with breath-hold task BOLD fMRI. Neuroimage 2023; 272:120038. [PMID: 36958618 DOI: 10.1016/j.neuroimage.2023.120038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/27/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
Cerebrovascular reactivity (CVR), defined as the cerebral blood flow response to a vasoactive stimulus, is an imaging biomarker with demonstrated utility in a range of diseases and in typical development and aging processes. A robust and widely implemented method to map CVR involves using a breath-hold task during a BOLD fMRI scan. Recording end-tidal CO2 (PETCO2) changes during the breath-hold task is recommended to be used as a reference signal for modeling CVR amplitude in standard units (%BOLD/mmHg) and CVR delay in seconds. However, obtaining reliable PETCO2 recordings requires equipment and task compliance that may not be achievable in all settings. To address this challenge, we investigated two alternative reference signals to map CVR amplitude and delay in a lagged general linear model (lagged-GLM) framework: respiration volume per time (RVT) and average gray matter BOLD response (GM-BOLD). In 8 healthy adults with multiple scan sessions, we compare spatial agreement of CVR maps from RVT and GM-BOLD to those generated with PETCO2. We define a threshold to determine whether a PETCO2 recording has "sufficient" quality for CVR mapping and perform these comparisons in 16 datasets with sufficient PETCO2 and 6 datasets with insufficient PETCO2. When PETCO2 quality is sufficient, both RVT and GM-BOLD produce CVR amplitude maps that are nearly identical to those from PETCO2 (after accounting for differences in scale), with the caveat they are not in standard units to facilitate between-group comparisons. CVR delays are comparable to PETCO2 with an RVT regressor but may be underestimated with the average GM-BOLD regressor. Importantly, when PETCO2 quality is insufficient, RVT and GM-BOLD CVR recover reasonable CVR amplitude and delay maps, provided the participant attempted the breath-hold task. Therefore, our framework offers a solution for achieving high quality CVR maps in both retrospective and prospective studies where sufficient PETCO2 recordings are not available and especially in populations where obtaining reliable measurements is a known challenge (e.g., children). Our results have the potential to improve the accessibility of CVR mapping and to increase the prevalence of this promising metric of vascular health.
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Affiliation(s)
- Kristina M Zvolanek
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA.
| | - Stefano Moia
- Basque Center on Cognition, Brain and Language, Donostia, Gipuzkoa, Spain; Medical Imaging Processing Lab (MIP:Lab), Neuro-X institute, EPFL, Geneva, Switzerland
| | - Joshua N Dean
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
| | - Rachael C Stickland
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Molly G Bright
- Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
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10
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Steel A, Garcia BD, Silson EH, Robertson CE. Evaluating the efficacy of multi-echo ICA denoising on model-based fMRI. Neuroimage 2022; 264:119723. [PMID: 36328274 DOI: 10.1016/j.neuroimage.2022.119723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/30/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022] Open
Abstract
fMRI is an indispensable tool for neuroscience investigation, but this technique is limited by multiple sources of physiological and measurement noise. These noise sources are particularly problematic for analysis techniques that require high signal-to-noise ratio for stable model fitting, such as voxel-wise modeling. Multi-echo data acquisition in combination with echo-time dependent ICA denoising (ME-ICA) represents one promising strategy to mitigate physiological and hardware-related noise sources as well as motion-related artifacts. However, most studies employing ME-ICA to date are resting-state fMRI studies, and therefore we have a limited understanding of the impact of ME-ICA on complex task or model-based fMRI paradigms. Here, we addressed this knowledge gap by comparing data quality and model fitting performance of data acquired during a visual population receptive field (pRF) mapping (N = 13 participants) experiment after applying one of three preprocessing procedures: ME-ICA, optimally combined multi-echo data without ICA-denoising, and typical single echo processing. As expected, multi-echo fMRI improved temporal signal-to-noise compared to single echo fMRI, with ME-ICA amplifying the improvement compared to optimal combination alone. However, unexpectedly, this boost in temporal signal-to-noise did not directly translate to improved model fitting performance: compared to single echo acquisition, model fitting was only improved after ICA-denoising. Specifically, compared to single echo acquisition, ME-ICA resulted in improved variance explained by our pRF model throughout the visual system, including anterior regions of the temporal and parietal lobes where SNR is typically low, while optimal combination without ICA did not. ME-ICA also improved reliability of parameter estimates compared to single echo and optimally combined multi-echo data without ICA-denoising. Collectively, these results suggest that ME-ICA is effective for denoising task-based fMRI data for modeling analyzes and maintains the integrity of the original data. Therefore, ME-ICA may be beneficial for complex fMRI experiments, including voxel-wise modeling and naturalistic paradigms.
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Affiliation(s)
- Adam Steel
- Department of Psychology and Brain Sciences, Dartmouth College, 3 Maynard Street, Hanover, NH 03755, US.
| | - Brenda D Garcia
- Department of Psychology and Brain Sciences, Dartmouth College, 3 Maynard Street, Hanover, NH 03755, US
| | - Edward H Silson
- Psychology, School of Philosophy, Psychology, and Language Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Caroline E Robertson
- Department of Psychology and Brain Sciences, Dartmouth College, 3 Maynard Street, Hanover, NH 03755, US
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11
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Can this data be saved? Techniques for high motion in resting state scans of first grade children. Dev Cogn Neurosci 2022; 58:101178. [PMID: 36434964 PMCID: PMC9694086 DOI: 10.1016/j.dcn.2022.101178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Motion remains a significant technical hurdle in fMRI studies of young children. Our aim was to develop a straightforward and effective method for obtaining and preprocessing resting state data from a high-motion pediatric cohort. This approach combines real-time monitoring of head motion with a preprocessing pipeline that uses volume censoring and concatenation alongside independent component analysis based denoising. We evaluated this method using a sample of 108 first grade children (age 6-8) enrolled in a longitudinal study of math development. Data quality was assessed by analyzing the correlation between participant head motion and two key metrics for resting state data, temporal signal-to-noise and functional connectivity. These correlations should be minimal in the absence of noise-related artifacts. We compared these data quality indicators using several censoring thresholds to determine the necessary degree of censoring. Volume censoring was highly effective at removing motion-corrupted volumes and ICA denoising removed much of the remaining motion artifact. With the censoring threshold set to exclude volumes that exceeded a framewise displacement of 0.3 mm, preprocessed data met rigorous standards for data quality while retaining a large majority of subjects (83 % of participants). Overall, results show it is possible to obtain usable resting-state data despite extreme motion in a group of young, untrained subjects.
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12
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Guilbert J, Légaré A, De Koninck P, Desrosiers P, Desjardins M. Toward an integrative neurovascular framework for studying brain networks. NEUROPHOTONICS 2022; 9:032211. [PMID: 35434179 PMCID: PMC8989057 DOI: 10.1117/1.nph.9.3.032211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/11/2022] [Indexed: 05/28/2023]
Abstract
Brain functional connectivity based on the measure of blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signals has become one of the most widely used measurements in human neuroimaging. However, the nature of the functional networks revealed by BOLD fMRI can be ambiguous, as highlighted by a recent series of experiments that have suggested that typical resting-state networks can be replicated from purely vascular or physiologically driven BOLD signals. After going through a brief review of the key concepts of brain network analysis, we explore how the vascular and neuronal systems interact to give rise to the brain functional networks measured with BOLD fMRI. This leads us to emphasize a view of the vascular network not only as a confounding element in fMRI but also as a functionally relevant system that is entangled with the neuronal network. To study the vascular and neuronal underpinnings of BOLD functional connectivity, we consider a combination of methodological avenues based on multiscale and multimodal optical imaging in mice, used in combination with computational models that allow the integration of vascular information to explain functional connectivity.
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Affiliation(s)
- Jérémie Guilbert
- Université Laval, Department of Physics, Physical Engineering, and Optics, Québec, Canada
- Université Laval, Centre de recherche du CHU de Québec, Québec, Canada
| | - Antoine Légaré
- Université Laval, Department of Physics, Physical Engineering, and Optics, Québec, Canada
- Centre de recherche CERVO, Québec, Canada
- Université Laval, Department of Biochemistry, Microbiology, and Bioinformatics, Québec, Canada
| | - Paul De Koninck
- Centre de recherche CERVO, Québec, Canada
- Université Laval, Department of Biochemistry, Microbiology, and Bioinformatics, Québec, Canada
| | - Patrick Desrosiers
- Université Laval, Department of Physics, Physical Engineering, and Optics, Québec, Canada
- Centre de recherche CERVO, Québec, Canada
| | - Michèle Desjardins
- Université Laval, Department of Physics, Physical Engineering, and Optics, Québec, Canada
- Université Laval, Centre de recherche du CHU de Québec, Québec, Canada
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13
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Wu GR, Colenbier N, Van Den Bossche S, Clauw K, Johri A, Tandon M, Marinazzo D. rsHRF: A toolbox for resting-state HRF estimation and deconvolution. Neuroimage 2021; 244:118591. [PMID: 34560269 DOI: 10.1016/j.neuroimage.2021.118591] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/25/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022] Open
Abstract
The hemodynamic response function (HRF) greatly influences the intra- and inter-subject variability of brain activation and connectivity, and might confound the estimation of temporal precedence in connectivity analyses, making its estimation necessary for a correct interpretation of neuroimaging studies. Additionally, the HRF shape itself is a useful local measure. However, most algorithms for HRF estimation are specific for task-related fMRI data, and only a few can be directly applied to resting-state protocols. Here we introduce rsHRF, a Matlab and Python toolbox that implements HRF estimation and deconvolution from the resting-state BOLD signal. We first provide an overview of the main algorithm, practical implementations, and then demonstrate the feasibility and usefulness of rsHRF by validation experiments with a publicly available resting-state fMRI dataset. We also provide tools for statistical analyses and visualization. We believe that this toolbox may significantly contribute to a better analysis and understanding of the components and variability of BOLD signals.
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Affiliation(s)
- Guo-Rong Wu
- Key Laboratory of Cognition and Personality, Faculty of Psychology, Southwest University, Chongqing 400715, China; Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent 9000, Belgium.
| | - Nigel Colenbier
- Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent 9000, Belgium; Research Center for Motor Control and Neuroplasticity, KU Leuven, Leuven 3001, Belgium; Brain Imaging and Neural Dynamics Research Group, IRCCS San Camillo Hospital, Venice 30126, Italy
| | - Sofie Van Den Bossche
- Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent 9000, Belgium
| | - Kenzo Clauw
- Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent 9000, Belgium
| | - Amogh Johri
- International Institute of Information Technology, Bangalore 560100, India
| | - Madhur Tandon
- Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Daniele Marinazzo
- Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent 9000, Belgium; Brain Imaging and Neural Dynamics Research Group, IRCCS San Camillo Hospital, Venice 30126, Italy
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14
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Dowdle LT, Ghose G, Chen CCC, Ugurbil K, Yacoub E, Vizioli L. Statistical power or more precise insights into neuro-temporal dynamics? Assessing the benefits of rapid temporal sampling in fMRI. Prog Neurobiol 2021; 207:102171. [PMID: 34492308 DOI: 10.1016/j.pneurobio.2021.102171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Functional magnetic resonance imaging (fMRI), a non-invasive and widely used human neuroimaging method, is most known for its spatial precision. However, there is a growing interest in its temporal sensitivity. This is despite the temporal blurring of neuronal events by the blood oxygen level dependent (BOLD) signal, the peak of which lags neuronal firing by 4-6 seconds. Given this, the goal of this review is to answer a seemingly simple question - "What are the benefits of increased temporal sampling for fMRI?". To answer this, we have combined fMRI data collected at multiple temporal scales, from 323 to 1000 milliseconds, with a review of both historical and contemporary temporal literature. After a brief discussion of technological developments that have rekindled interest in temporal research, we next consider the potential statistical and methodological benefits. Most importantly, we explore how fast fMRI can uncover previously unobserved neuro-temporal dynamics - effects that are entirely missed when sampling at conventional 1 to 2 second rates. With the intrinsic link between space and time in fMRI, this temporal renaissance also delivers improvements in spatial precision. Far from producing only statistical gains, the array of benefits suggest that the continued temporal work is worth the effort.
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Affiliation(s)
- Logan T Dowdle
- Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN, 55455, United States; Department of Neurosurgery, University of Minnesota, 500 SE Harvard St, Minneapolis, MN, 55455, United States; Department of Neuroscience, University of Minnesota, 321 Church St SE, Minneapolis, MN, 55455, United States.
| | - Geoffrey Ghose
- Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN, 55455, United States; Department of Neuroscience, University of Minnesota, 321 Church St SE, Minneapolis, MN, 55455, United States
| | - Clark C C Chen
- Department of Neurosurgery, University of Minnesota, 500 SE Harvard St, Minneapolis, MN, 55455, United States
| | - Kamil Ugurbil
- Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN, 55455, United States
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN, 55455, United States
| | - Luca Vizioli
- Center for Magnetic Resonance Research, University of Minnesota, 2021 6th St SE, Minneapolis, MN, 55455, United States; Department of Neurosurgery, University of Minnesota, 500 SE Harvard St, Minneapolis, MN, 55455, United States.
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15
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Stickland RC, Zvolanek KM, Moia S, Ayyagari A, Caballero-Gaudes C, Bright MG. A practical modification to a resting state fMRI protocol for improved characterization of cerebrovascular function. Neuroimage 2021; 239:118306. [PMID: 34175427 PMCID: PMC8552969 DOI: 10.1016/j.neuroimage.2021.118306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022] Open
Abstract
Cerebrovascular reactivity (CVR), defined here as the Blood Oxygenation Level Dependent (BOLD) response to a CO2 pressure change, is a useful metric of cerebrovascular function. Both the amplitude and the timing (hemodynamic lag) of the CVR response can bring insight into the nature of a cerebrovascular pathology and aid in understanding noise confounds when using functional Magnetic Resonance Imaging (fMRI) to study neural activity. This research assessed a practical modification to a typical resting-state fMRI protocol, to improve the characterization of cerebrovascular function. In 9 healthy subjects, we modelled CVR and lag in three resting-state data segments, and in data segments which added a 2–3 minute breathing task to the start of a resting-state segment. Two different breathing tasks were used to induce fluctuations in arterial CO2 pressure: a breath-hold task to induce hypercapnia (CO2 increase) and a cued deep breathing task to induce hypocapnia (CO2 decrease). Our analysis produced voxel-wise estimates of the amplitude (CVR) and timing (lag) of the BOLD-fMRI response to CO2 by systematically shifting the CO2 regressor in time to optimize the model fit. This optimization inherently increases gray matter CVR values and fit statistics. The inclusion of a simple breathing task, compared to a resting-state scan only, increases the number of voxels in the brain that have a significant relationship between CO2 and BOLD-fMRI signals, and improves our confidence in the plausibility of voxel-wise CVR and hemodynamic lag estimates. We demonstrate the clinical utility and feasibility of this protocol in an incidental finding of Moyamoya disease, and explore the possibilities and challenges of using this protocol in younger populations. This hybrid protocol has direct applications for CVR mapping in both research and clinical settings and wider applications for fMRI denoising and interpretation.
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Affiliation(s)
- Rachael C Stickland
- Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.
| | - Kristina M Zvolanek
- 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
| | - Stefano Moia
- Basque Center on Cognition, Brain and Language, Donostia, Gipuzkoa, Spain; University of the Basque Country EHU/UPV, Donostia, Gipuzkoa, Spain
| | - Apoorva Ayyagari
- 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
| | | | - 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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16
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Lynch CJ, Elbau I, Liston C. Improving precision functional mapping routines with multi-echo fMRI. Curr Opin Behav Sci 2021; 40:113-119. [PMID: 34095359 DOI: 10.1016/j.cobeha.2021.03.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rapidly developing approaches to acquiring and analyzing densely-sampled, single-subject fMRI data have opened new avenues for understanding the neurobiological basis of individual differences in behavior and could allow fMRI to become a more clinically useful tool. Here, we review briefly key insights from these precision functional mapping studies and a highlight significant barrier to their clinical translation. Specifically, that reliable delineation of functional brain networks in individual humans can require hours of resting-state fMRI data per-subject. We found recently that multi-echo fMRI improves the test-retest reliability of resting-state functional connectivity measurements, mitigating the need for acquiring large quantities of per -subject data. Because the benefits of multi-echo acquisitions are most pronounced in clinically important but artifact-prone brain regions, such as the subgenual cingulate and structures deep in the subcortex, this approach has the potential to increase the impact of precision functional mapping routines in both healthy and clinical populations.
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Affiliation(s)
- Charles J Lynch
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, 413 East 69 Street, Box 240, New York, NY 10021
| | - Immanuel Elbau
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, 413 East 69 Street, Box 240, New York, NY 10021
| | - Conor Liston
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, 413 East 69 Street, Box 240, New York, NY 10021
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