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Bright MG, Tench CR, Murphy K. Potential pitfalls when denoising resting state fMRI data using nuisance regression. Neuroimage 2016; 154:159-168. [PMID: 28025128 PMCID: PMC5489212 DOI: 10.1016/j.neuroimage.2016.12.027] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/07/2016] [Accepted: 12/10/2016] [Indexed: 12/15/2022] Open
Abstract
In resting state fMRI, it is necessary to remove signal variance associated with noise sources, leaving cleaned fMRI time-series that more accurately reflect the underlying intrinsic brain fluctuations of interest. This is commonly achieved through nuisance regression, in which the fit is calculated of a noise model of head motion and physiological processes to the fMRI data in a General Linear Model, and the "cleaned" residuals of this fit are used in further analysis. We examine the statistical assumptions and requirements of the General Linear Model, and whether these are met during nuisance regression of resting state fMRI data. Using toy examples and real data we show how pre-whitening, temporal filtering and temporal shifting of regressors impact model fit. Based on our own observations, existing literature, and statistical theory, we make the following recommendations when employing nuisance regression: pre-whitening should be applied to achieve valid statistical inference of the noise model fit parameters; temporal filtering should be incorporated into the noise model to best account for changes in degrees of freedom; temporal shifting of regressors, although merited, should be achieved via optimisation and validation of a single temporal shift. We encourage all readers to make simple, practical changes to their fMRI denoising pipeline, and to regularly assess the appropriateness of the noise model used. By negotiating the potential pitfalls described in this paper, and by clearly reporting the details of nuisance regression in future manuscripts, we hope that the field will achieve more accurate and precise noise models for cleaning the resting state fMRI time-series.
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Affiliation(s)
- Molly G Bright
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom; Division of Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom.
| | - Christopher R Tench
- Division of Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Kevin Murphy
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom; CUBRIC, School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
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Donahue MJ, Strother MK, Lindsey KP, Hocke LM, Tong Y, Frederick BD. Time delay processing of hypercapnic fMRI allows quantitative parameterization of cerebrovascular reactivity and blood flow delays. J Cereb Blood Flow Metab 2016; 36:1767-1779. [PMID: 26661192 PMCID: PMC5076782 DOI: 10.1177/0271678x15608643] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/29/2015] [Indexed: 11/17/2022]
Abstract
Blood oxygenation level-dependent fMRI contrast depends on the volume and oxygenation of blood flowing through the circulatory system. The effects on image intensity depend temporally on the arrival of blood within a voxel, and signal can be monitored during the time course of such blood flow. It has been previously shown that the passage of global endogenous variations in blood volume and oxygenation can be tracked as blood passes through the brain by determining the strength and peak time lag of their cross-correlation with blood oxygenation level-dependent data. By manipulating blood composition using transient hypercarbia and hyperoxia, we can induce much larger oxygenation and volume changes in the blood oxygenation level-dependent signal than result from natural endogenous fluctuations. This technique was used to examine cerebrovascular parameters in healthy subjects (n = 8) and subjects with intracranial stenosis (n = 22), with a subgroup of intracranial stenosis subjects scanned before and after surgical revascularization (n = 6). The halfwidth of cross-correlation lag times in the brain was larger in IC stenosis subjects (21.21 ± 14.22 s) than in healthy control subjects (8.03 ± 3.67), p < 0.001, and was subsequently reduced in regions that co-localized with surgical revascularization. These data show that blood circulatory timing can be measured robustly and longitudinally throughout the brain using simple respiratory challenges.
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Affiliation(s)
- Manus J Donahue
- Department of Radiology, Vanderbilt Medical Center, Nashville, TN, USA Department of Neurology, Vanderbilt Medical Center, Nashville, TN, USA Department of Psychiatry, Vanderbilt Medical Center, Nashville, TN, USA Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, USA
| | - Megan K Strother
- Department of Radiology, Vanderbilt Medical Center, Nashville, TN, USA
| | - Kimberly P Lindsey
- Brain Imaging Center, McLean Hospital, Belmont, MA, USA Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Lia M Hocke
- Brain Imaging Center, McLean Hospital, Belmont, MA, USA Department of Bioengineering, Tufts University, Medford, MA, USA
| | - Yunjie Tong
- Brain Imaging Center, McLean Hospital, Belmont, MA, USA Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Blaise deB Frederick
- Brain Imaging Center, McLean Hospital, Belmont, MA, USA Department of Psychiatry, Harvard Medical School, Boston, MA, USA
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103
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Rane S, Koh N, Boord P, Askren MK, Gatenby JC, Madhyashtha TM, Mestre Z, Grabowski TJ. P1‐248: Cerebrovascular Reserve as a Marker of Vascular Pathology and Cognitive Status in Older ADULTS. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Swati Rane
- University of Washington Medical CenterSeattleWA USA
| | - Natalie Koh
- University of Washington Medical CenterSeattleWA USA
| | - Peter Boord
- University of Washington Medical CenterSeattleWA USA
| | | | | | | | - Zoe Mestre
- University of Washington Medical CenterSeattleWA USA
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104
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Tan CH, Low KA, Schneider-Garces N, Zimmerman B, Fletcher MA, Maclin EL, Chiarelli AM, Gratton G, Fabiani M. Optical measures of changes in cerebral vascular tone during voluntary breath holding and a Sternberg memory task. Biol Psychol 2016; 118:184-194. [PMID: 27235126 PMCID: PMC9906974 DOI: 10.1016/j.biopsycho.2016.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 12/24/2022]
Abstract
The human cerebral vasculature responds to changes in blood pressure and demands for oxygenation via cerebral autoregulation. Changes in cerebrovascular tone (vasoconstriction and vasodilation) also mediate the changes in blood flow measured by the BOLD fMRI signal. This cerebrovascular reactivity is known to vary with age. In two experiments, we demonstrate that cerebral pulse parameters measured using optical imaging can quantify changes in cerebral vascular tone, both globally and locally. In experiment 1, 51 older adults (age range=55-87) performed a voluntary breath-holding task while cerebral pulse amplitude measures were taken. We found significant pulse amplitude variations across breath-holding periods, indicating vasodilation during, and vasoconstriction after breath holding. The breath-holding index (BHI), a measure of cerebrovascular reactivity (CVR) was derived and found to correlate with age. BHI was also correlated with performance in the Modified Mini-Mental Status Examination, even after controlling for age and education. In experiment 2, the same participants performed a Sternberg task, and changes in regional pulse amplitude between high (set-size 6) and low (set-size 2) task loads were compared. Only task-related areas in the fronto-parietal network (FPN) showed significant reduction in pulse amplitude, indicating vasodilation. Non-task-related areas such as the somatosensory and auditory cortices did not show such reductions. Taken together, these experiments suggest that optical pulse parameters can index changes in brain vascular tone both globally and locally, using both physiological and cognitive load manipulations.
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Affiliation(s)
- Chin Hong Tan
- Department of Psychology, University of Illinois at Urbana-Champaign, United States,Beckman Institute, University of Illinois at Urbana-Champaign, United States
| | - Kathy A. Low
- Beckman Institute, University of Illinois at Urbana-Champaign, United States
| | | | - Benjamin Zimmerman
- Beckman Institute, University of Illinois at Urbana-Champaign, United States
| | - Mark A. Fletcher
- Beckman Institute, University of Illinois at Urbana-Champaign, United States
| | - Edward L. Maclin
- Beckman Institute, University of Illinois at Urbana-Champaign, United States
| | | | - Gabriele Gratton
- Department of Psychology, University of Illinois at Urbana-Champaign, United States,Beckman Institute, University of Illinois at Urbana-Champaign, United States
| | - Monica Fabiani
- Department of Psychology, University of Illinois at Urbana-Champaign, United States; Beckman Institute, University of Illinois at Urbana-Champaign, United States.
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105
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Hypercapnic evaluation of vascular reactivity in healthy aging and acute stroke via functional MRI. NEUROIMAGE-CLINICAL 2016; 12:173-9. [PMID: 27437178 PMCID: PMC4939388 DOI: 10.1016/j.nicl.2016.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/26/2016] [Accepted: 06/22/2016] [Indexed: 11/23/2022]
Abstract
Functional MRI (fMRI) is well-established for the study of brain function in healthy populations, although its clinical application has proven more challenging. Specifically, cerebrovascular reactivity (CVR), which allows the assessment of the vascular response that serves as the basis for fMRI, has been shown to be reduced in healthy aging as well as in a range of diseases, including chronic stroke. However, the timing of when this occurs relative to the stroke event is unclear. We used a breath-hold fMRI task to evaluate CVR across gray matter in a group of acute stroke patients (< 10 days from stroke; N = 22) to address this question. These estimates were compared with those from both age-matched (N = 22) and younger (N = 22) healthy controls. As expected, young controls had the greatest mean CVR, as indicated by magnitude and extent of fMRI activation; however, stroke patients did not differ from age-matched controls. Moreover, the ipsilesional and contralesional hemispheres of stroke patients did not differ with respect to any of these measures. These findings suggest that fMRI remains a valid tool within the first few days of a stroke, particularly for group fMRI studies in which findings are compared with healthy subjects of similar age. However, given the relatively high variability in CVR observed in our stroke sample, caution is warranted when interpreting fMRI data from individual patients or a small cohort. We conclude that a breath-hold task can be a useful addition to functional imaging protocols for stroke patients. Breath-holding can be used to assess the validity of fMRI in stroke patients. Vascular reactivity, estimated by breath-hold fMRI, was greatest in young controls. Acute stroke patients and age-matched controls had similar vascular reactivity. Modeling the breath-hold response on an individual basis can improve results.
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106
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Bhogal AA, De Vis JB, Siero JCW, Petersen ET, Luijten PR, Hendrikse J, Philippens MEP, Hoogduin H. The BOLD cerebrovascular reactivity response to progressive hypercapnia in young and elderly. Neuroimage 2016; 139:94-102. [PMID: 27291492 DOI: 10.1016/j.neuroimage.2016.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/30/2016] [Accepted: 06/08/2016] [Indexed: 12/01/2022] Open
Abstract
Blood Oxygenation Level Dependent (BOLD) imaging in combination with vasoactive stimuli can be used to probe cerebrovascular reactivity (CVR). Characterizing the healthy, age-related changes in the BOLD-CVR response can provide a reference point from which to distinguish abnormal CVR from the otherwise normal effects of ageing. Using a computer controlled gas delivery system, we examine differences in BOLD-CVR response to progressive hypercapnia between 16 young (28±3years, 9 female) and 30 elderly subjects (66±4years, 13 female). Furthermore, we incorporate baseline T2* information to broaden our interpretation of the BOLD-CVR response. Significant age-related differences were observed. Grey matter CVR at 7mmHg above resting PetCO2 was lower amongst elderly (0.19±0.06%ΔBOLD/mmHg) as compared to young subjects (0.26±0.07%ΔBOLD/mmHg). White matter CVR at 7mmHg above baseline PetCO2 showed no significant difference between young (0.04±0.02%ΔBOLD/mmHg) and elderly subjects (0.05±0.03%ΔBOLD/mmHg). We saw no significant differences in the BOLD signal response to progressive hypercapnia between male and female subjects in either grey or white matter. The observed differences in the healthy BOLD-CVR response could be explained by age-related changes in vascular mechanical properties.
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Affiliation(s)
- Alex A Bhogal
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Jill B De Vis
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen C W Siero
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Esben T Petersen
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital, Hvidovre, Denmark
| | - Peter R Luijten
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen Hendrikse
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Hans Hoogduin
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
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107
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Respiratory challenge MRI: Practical aspects. NEUROIMAGE-CLINICAL 2016; 11:667-677. [PMID: 27330967 PMCID: PMC4901170 DOI: 10.1016/j.nicl.2016.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/11/2016] [Accepted: 05/03/2016] [Indexed: 11/24/2022]
Abstract
Respiratory challenge MRI is the modification of arterial oxygen (PaO2) and/or carbon dioxide (PaCO2) concentration to induce a change in cerebral function or metabolism which is then measured by MRI. Alterations in arterial gas concentrations can lead to profound changes in cerebral haemodynamics which can be studied using a variety of MRI sequences. Whilst such experiments may provide a wealth of information, conducting them can be complex and challenging. In this paper we review the rationale for respiratory challenge MRI including the effects of oxygen and carbon dioxide on the cerebral circulation. We also discuss the planning, equipment, monitoring and techniques that have been used to undertake these experiments. We finally propose some recommendations in this evolving area for conducting these experiments to enhance data quality and comparison between techniques. Oxygen and carbon dioxide affect cerebral blood flow and metabolism. This can be imaged with various MRI sequences. The practicalities of these techniques are reviewed. Examples of how this has been used to understand disease mechanisms.
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108
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Fierstra J, Burkhardt JK, van Niftrik CHB, Piccirelli M, Pangalu A, Kocian R, Neidert MC, Valavanis A, Regli L, Bozinov O. Blood oxygen-level dependent functional assessment of cerebrovascular reactivity: Feasibility for intraoperative 3 Tesla MRI. Magn Reson Med 2016; 77:806-813. [PMID: 26918794 DOI: 10.1002/mrm.26135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/29/2015] [Accepted: 12/26/2015] [Indexed: 11/10/2022]
Abstract
PURPOSE To assess the feasibility of functional blood oxygen-level dependent (BOLD) MRI to evaluate intraoperative cerebrovascular reactivity (CVR) at 3 Tesla field strength. METHODS Ten consecutive neurosurgical subjects scheduled for a clinical intraoperative MRI examination were enrolled in this study. In addition to the clinical protocol a BOLD sequence was implemented with three cycles of 44 s apnea to calculate CVR values on a voxel-by-voxel basis throughout the brain. The CVR range was then color-coded and superimposed on an anatomical volume to create high spatial resolution CVR maps. RESULTS Ten subjects (mean age 34.8 ± 13.4; 2 females) uneventfully underwent the intraoperative BOLD protocol, with no complications occurring. Whole-brain CVR for all subjects was (mean ± SD) 0.69 ± 0.42, whereas CVR was markedly higher for tumor subjects as compared to vascular subjects, 0.81 ± 0.44 versus 0.33 ± 0.10, respectively. Furthermore, color-coded functional maps could be robustly interpreted for a whole-brain assessment of CVR. CONCLUSION We demonstrate that intraoperative BOLD MRI is feasible in creating functional maps to assess cerebrovascular reactivity throughout the brain in subjects undergoing a neurosurgical procedure. Magn Reson Med 77:806-813, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Jorn Fierstra
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Jan-Karl Burkhardt
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | | | - Marco Piccirelli
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Athina Pangalu
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Roman Kocian
- Department of Neuro-anesthesia, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Marian Christoph Neidert
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Antonios Valavanis
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Luca Regli
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Oliver Bozinov
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Switzerland
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Pinto J, Jorge J, Sousa I, Vilela P, Figueiredo P. Fourier modeling of the BOLD response to a breath-hold task: Optimization and reproducibility. Neuroimage 2016; 135:223-31. [PMID: 26908316 DOI: 10.1016/j.neuroimage.2016.02.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/09/2016] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Cerebrovascular reactivity (CVR) reflects the capacity of blood vessels to adjust their caliber in order to maintain a steady supply of brain perfusion, and it may provide a sensitive disease biomarker. Measurement of the blood oxygen level dependent (BOLD) response to a hypercapnia-inducing breath-hold (BH) task has been frequently used to map CVR noninvasively using functional magnetic resonance imaging (fMRI). However, the best modeling approach for the accurate quantification of CVR maps remains an open issue. Here, we compare and optimize Fourier models of the BOLD response to a BH task with a preparatory inspiration, and assess the test-retest reproducibility of the associated CVR measurements, in a group of 10 healthy volunteers studied over two fMRI sessions. Linear combinations of sine-cosine pairs at the BH task frequency and its successive harmonics were added sequentially in a nested models approach, and were compared in terms of the adjusted coefficient of determination and corresponding variance explained (VE) of the BOLD signal, as well as the number of voxels exhibiting significant BOLD responses, the estimated CVR values, and their test-retest reproducibility. The brain average VE increased significantly with the Fourier model order, up to the 3rd order. However, the number of responsive voxels increased significantly only up to the 2nd order, and started to decrease from the 3rd order onwards. Moreover, no significant relative underestimation of CVR values was observed beyond the 2nd order. Hence, the 2nd order model was concluded to be the optimal choice for the studied paradigm. This model also yielded the best test-retest reproducibility results, with intra-subject coefficients of variation of 12 and 16% and an intra-class correlation coefficient of 0.74. In conclusion, our results indicate that a Fourier series set consisting of a sine-cosine pair at the BH task frequency and its two harmonics is a suitable model for BOLD-fMRI CVR measurements based on a BH task with preparatory inspiration, yielding robust estimates of this important physiological parameter.
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Affiliation(s)
- Joana Pinto
- Institute for Systems and Robotics, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| | - João Jorge
- Institute for Systems and Robotics, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Biomedical Imaging Research Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Inês Sousa
- Institute for Systems and Robotics, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Healthcare Sector, Siemens, S.A., Portugal
| | - Pedro Vilela
- Imaging Department, Hospital da Luz, Lisbon, Portugal
| | - Patrícia Figueiredo
- Institute for Systems and Robotics, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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van Niftrik CHB, Piccirelli M, Bozinov O, Pangalu A, Valavanis A, Regli L, Fierstra J. Fine tuning breath-hold-based cerebrovascular reactivity analysis models. Brain Behav 2016; 6:e00426. [PMID: 27110448 PMCID: PMC4834934 DOI: 10.1002/brb3.426] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 11/25/2015] [Accepted: 12/07/2015] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION We elaborate on existing analysis methods for breath-hold (BH)-derived cerebrovascular reactivity (CVR) measurements and describe novel insights and models toward more exact CVR interpretation. METHODS Five blood-oxygen-level-dependent (BOLD) fMRI datasets of neurovascular patients with unilateral hemispheric hemodynamic impairment were used to test various BH CVR analysis methods. Temporal lag (phase), percent BOLD signal change (CVR), and explained variance (coherence) maps were calculated using three different sine models and two novel "Optimal Signal" model-free methods based on the unaffected hemisphere and the sagittal sinus fMRI signal time series, respectively. RESULTS All models showed significant differences in CVR and coherence between the affected-hemodynamic impaired-and unaffected hemisphere. Voxel-wise phase determination significantly increases CVR (0.60 ± 0.18 vs. 0.82 ± 0.27; P < 0.05). Incorporating different durations of breath hold and resting period in one sine model (two-task) did increase coherence in the unaffected hemisphere, as well as eliminating negative phase commonly obtained by one-task frequency models. The novel model-free "optimal signal" methods both explained the BOLD MR data similar to the two task sine model. CONCLUSIONS Our CVR analysis demonstrates an improved CVR and coherence after implementation of voxel-wise phase and frequency adjustment. The novel "optimal signal" methods provide a robust and feasible alternative to the sine models, as both are model-free and independent of compliance. Here, the sagittal sinus model may be advantageous, as it is independent of hemispheric CVR impairment.
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Affiliation(s)
- Christiaan Hendrik Bas van Niftrik
- Department of Neurosurgery University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
| | - Marco Piccirelli
- Department of Neuroradiology University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
| | - Oliver Bozinov
- Department of Neurosurgery University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
| | - Athina Pangalu
- Department of Neuroradiology University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
| | - Antonios Valavanis
- Department of Neuroradiology University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
| | - Luca Regli
- Department of Neurosurgery University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
| | - Jorn Fierstra
- Department of Neurosurgery University Hospital Zurich University of Zurich Clinical Neuroscience Center Frauenklinikstrasse 10 8091 Zurich Switzerland
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Svaldi DO, McCuen EC, Joshi C, Robinson ME, Nho Y, Hannemann R, Nauman EA, Leverenz LJ, Talavage TM. Cerebrovascular reactivity changes in asymptomatic female athletes attributable to high school soccer participation. Brain Imaging Behav 2016; 11:98-112. [DOI: 10.1007/s11682-016-9509-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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112
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Bright MG, Murphy K. Is fMRI "noise" really noise? Resting state nuisance regressors remove variance with network structure. Neuroimage 2015; 114:158-69. [PMID: 25862264 PMCID: PMC4461310 DOI: 10.1016/j.neuroimage.2015.03.070] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 03/10/2015] [Accepted: 03/27/2015] [Indexed: 12/01/2022] Open
Abstract
Noise correction is a critical step towards accurate mapping of resting state BOLD fMRI connectivity. Noise sources related to head motion or physiology are typically modelled by nuisance regressors, and a generalised linear model is applied to regress out the associated signal variance. In this study, we use independent component analysis (ICA) to characterise the data variance typically discarded in this pre-processing stage in a cohort of 12 healthy volunteers. The signal variance removed by 24, 12, 6, or only 3 head motion parameters demonstrated network structure typically associated with functional connectivity, and certain networks were discernable in the variance extracted by as few as 2 physiologic regressors. Simulated nuisance regressors, unrelated to the true data noise, also removed variance with network structure, indicating that any group of regressors that randomly sample variance may remove highly structured “signal” as well as “noise.” Furthermore, to support this we demonstrate that random sampling of the original data variance continues to exhibit robust network structure, even when as few as 10% of the original volumes are considered. Finally, we examine the diminishing returns of increasing the number of nuisance regressors used in pre-processing, showing that excessive use of motion regressors may do little better than chance in removing variance within a functional network. It remains an open challenge to understand the balance between the benefits and confounds of noise correction using nuisance regressors. Data variance removed by nuisance regressors contains network structure. Simulated regressors unrelated to noise also extract data with network structure. Random sampling of original data (as few as 10% of volumes) reveals robust networks. After optimal number, motion regressors remove similar variance as simulated ones. Excessive nuisance regressors extract random signal variance with network structure.
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Affiliation(s)
- Molly G Bright
- Division of Clinical Neurology, School of Medicine, University of Nottingham, Nottingham, United Kingdom; Sir Peter Mansfield Imaging Centre, School of Physics, University of Nottingham, Nottingham, United Kingdom; Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.
| | - Kevin Murphy
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
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113
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Agreement and repeatability of vascular reactivity estimates based on a breath-hold task and a resting state scan. Neuroimage 2015; 113:387-96. [PMID: 25795342 PMCID: PMC4441043 DOI: 10.1016/j.neuroimage.2015.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 12/02/2022] Open
Abstract
FMRI BOLD responses to changes in neural activity are influenced by the reactivity of the vasculature. By complementing a task-related BOLD acquisition with a vascular reactivity measure obtained through breath-holding or hypercapnia, this unwanted variance can be statistically reduced in the BOLD responses of interest. Recently, it has been suggested that vascular reactivity can also be estimated using a resting state scan. This study aimed to compare three breath-hold based analysis approaches (block design, sine–cosine regressor and CO2 regressor) and a resting state approach (CO2 regressor) to measure vascular reactivity. We tested BOLD variance explained by the model and repeatability of the measures. Fifteen healthy participants underwent a breath-hold task and a resting state scan with end-tidal CO2 being recorded during both. Vascular reactivity was defined as CO2-related BOLD percent signal change/mm Hg change in CO2. Maps and regional vascular reactivity estimates showed high repeatability when the breath-hold task was used. Repeatability and variance explained by the CO2 trace regressor were lower for the resting state data based approach, which resulted in highly variable measures of vascular reactivity. We conclude that breath-hold based vascular reactivity estimations are more repeatable than resting-based estimates, and that there are limitations with replacing breath-hold scans by resting state scans for vascular reactivity assessment.
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Geranmayeh F, Wise RJS, Leech R, Murphy K. Measuring vascular reactivity with breath-holds after stroke: a method to aid interpretation of group-level BOLD signal changes in longitudinal fMRI studies. Hum Brain Mapp 2015; 36:1755-71. [PMID: 25727648 PMCID: PMC4413362 DOI: 10.1002/hbm.22735] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/12/2014] [Accepted: 01/05/2015] [Indexed: 11/20/2022] Open
Abstract
Blood oxygenation level‐dependent (BOLD) contrast functional magnetic resonance imaging (fMRI) is a widely used technique to map brain function, and to monitor its recovery after stroke. Since stroke has a vascular etiology, the neurovascular coupling between cerebral blood flow and neural activity may be altered, resulting in uncertainties when interpreting longitudinal BOLD signal changes. The purpose of this study was to demonstrate the feasibility of using a recently validated breath‐hold task in patients with stroke, both to assess group level changes in cerebrovascular reactivity (CVR) and to determine if alterations in regional CVR over time will adversely affect interpretation of task‐related BOLD signal changes. Three methods of analyzing the breath‐hold data were evaluated. The CVR measures were compared over healthy tissue, infarcted tissue and the peri‐infarct tissue, both sub‐acutely (∼2 weeks) and chronically (∼4 months). In this cohort, a lack of CVR differences in healthy tissue between the patients and controls indicates that any group level BOLD signal change observed in these regions over time is unlikely to be related to vascular alterations. CVR was reduced in the peri‐infarct tissue but remained unchanged over time. Therefore, although a lack of activation in this region compared with the controls may be confounded by a reduced CVR, longitudinal group‐level BOLD changes may be more confidently attributed to neural activity changes in this cohort. By including this breath‐hold‐based CVR assessment protocol in future studies of stroke recovery, researchers can be more assured that longitudinal changes in BOLD signal reflect true alterations in neural activity. Hum Brain Mapp 36:1755–1771, 2015. © 2015 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Fatemeh Geranmayeh
- Computational Cognitive and Clinical Neuroimaging Laboratory, Imperial College, Hammersmith Hospital, London, W12 0NN, United Kingdom
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115
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Comparing cerebrovascular reactivity measured using BOLD and cerebral blood flow MRI: The effect of basal vascular tension on vasodilatory and vasoconstrictive reactivity. Neuroimage 2015; 110:110-23. [PMID: 25655446 DOI: 10.1016/j.neuroimage.2015.01.050] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/15/2015] [Accepted: 01/26/2015] [Indexed: 11/23/2022] Open
Abstract
Cerebrovascular reactivity (CVR) is an important metric of cerebrovascular health. While the BOLD fMRI method in conjunction with carbon-dioxide (CO2) based vascular manipulation has been the most commonly used, the BOLD signal is not a direct measure of vascular changes, and the use of arterial-spin labeling (ASL) cerebral blood flow (CBF) imaging is increasingly advocated. Nonetheless, given the differing dependencies of BOLD and CBF on vascular baseline conditions and the diverse CO2 manipulation types currently used in the literature, knowledge of potential biases introduced by each technique is critical for the interpretation of CVR measurements. In this work, we use simultaneous BOLD-CBF acquisitions during both vasodilatory (hypercapnic) and vasoconstrictive (hypocapnic) stimuli to measure CVR. We further imposed different levels of baseline vascular tension by inducing hypercapnic and hypocapnic baselines, separately from normocapnia by 4mmHg. We saw significant and diverse dependencies on vascular stimulus and baseline condition in both BOLD and CBF CVR measurements: (i) BOLD-based CVR is more sensitive to basal vascular tension than CBF-based CVR; (ii) the use of a combination of vasodilatory and vasoconstrictive stimuli maximizes the sensitivity of CBF-based CVR to vascular tension changes; (iii) the BOLD and CBF vascular response delays are both significantly lengthened at predilated baseline. As vascular tension can often be altered by potential pathology, our findings are important considerations when interpreting CVR measurements in health and disease.
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116
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Reproducibility of hypocapnic cerebrovascular reactivity measurements using BOLD fMRI in combination with a paced deep breathing task. Neuroimage 2014; 98:31-41. [DOI: 10.1016/j.neuroimage.2014.04.049] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 11/23/2022] Open
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Regan RE, Fisher JA, Duffin J. Factors affecting the determination of cerebrovascular reactivity. Brain Behav 2014; 4:775-88. [PMID: 25328852 PMCID: PMC4188369 DOI: 10.1002/brb3.275] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/14/2014] [Accepted: 07/27/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND PURPOSE Cerebrovascular reactivity (CVR), measures the ability of the cerebrovasculature to respond to vasoactive stimuli such as CO2. CVR is often expressed as the ratio of cerebral blood flow change to CO2 change. We examine several factors affecting this measurement: blood pressure, stimulus pattern, response analysis and subject position. METHODS Step and ramp increases in CO2 were implemented in nine subjects, seated and supine. Middle cerebral artery blood flow velocity (MCAv), and mean arterial pressure (MAP) were determined breath-by-breath. Cerebrovascular conductance (MCAc) was estimated as MCAv/MAP. CVR was calculated from both the relative and absolute measures of MCAc and MCAv responses. RESULTS MAP increased with CO2 in some subjects so that relative CVR calculated from conductance responses were less than those calculated from CVR calculated from velocity responses. CVR measured from step responses were affected by the response dynamics, and were less than those calculated from CVR measured from ramp responses. Subject position did not affect CVR. CONCLUSIONS (1) MAP increases with CO2 and acts as a confounding factor for CVR measurement; (2) CVR depends on the stimulus pattern used; (3) CVR did not differ from the sitting versus supine in these experiments; (4) CVR calculated from absolute changes of MCAv was less than that calculated from relative changes.
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Affiliation(s)
- Rosemary E Regan
- Department of Physiology, University of Toronto Toronto, ON, M5S 1A8, Canada
| | - Joseph A Fisher
- Department of Physiology, University of Toronto Toronto, ON, M5S 1A8, Canada ; Department of Anaesthesiology, University of Toronto Toronto, ON, Canada ; University Health Network Toronto, ON, Canada
| | - James Duffin
- Department of Physiology, University of Toronto Toronto, ON, M5S 1A8, Canada ; Department of Anaesthesiology, University of Toronto Toronto, ON, Canada ; University Health Network Toronto, ON, Canada
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118
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Zuo XN, Xing XX. Test-retest reliabilities of resting-state FMRI measurements in human brain functional connectomics: a systems neuroscience perspective. Neurosci Biobehav Rev 2014; 45:100-18. [PMID: 24875392 DOI: 10.1016/j.neubiorev.2014.05.009] [Citation(s) in RCA: 467] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 12/20/2022]
Abstract
Resting-state functional magnetic resonance imaging (RFMRI) enables researchers to monitor fluctuations in the spontaneous brain activities of thousands of regions in the human brain simultaneously, representing a popular tool for macro-scale functional connectomics to characterize normal brain function, mind-brain associations, and the various disorders. However, the test-retest reliability of RFMRI remains largely unknown. We review previously published papers on the test-retest reliability of voxel-wise metrics and conduct a meta-summary reliability analysis of seven common brain networks. This analysis revealed that the heteromodal associative (default, control, and attention) networks were mostly reliable across the seven networks. Regarding examined metrics, independent component analysis with dual regression, local functional homogeneity and functional homotopic connectivity were the three mostly reliable RFMRI metrics. These observations can guide the use of reliable metrics and further improvement of test-retest reliability for other metics in functional connectomics. We discuss the main issues with low reliability related to sub-optimal design and the choice of data processing options. Future research should use large-sample test-retest data to rectify both the within-subject and between-subject variability of RFMRI measurements and accelerate the application of functional connectomics.
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Affiliation(s)
- Xi-Nian Zuo
- Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China; Laboratory for Functional Connectome and Development, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China; Magnetic Resonance Imaging Research Center, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiu-Xia Xing
- College of Applied Sciences, Beijing University of Technology, Beijing 100124, China.
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119
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Pillai JJ, Mikulis DJ. Cerebrovascular reactivity mapping: an evolving standard for clinical functional imaging. AJNR Am J Neuroradiol 2014; 36:7-13. [PMID: 24788129 DOI: 10.3174/ajnr.a3941] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
SUMMARY This review article explains the methodology of breath-hold cerebrovascular reactivity mapping, both in terms of acquisition and analysis, and reviews applications of this method to presurgical mapping, particularly with respect to blood oxygen level-dependent fMRI. Its main application in clinical fMRI is for the assessment of neurovascular uncoupling potential. Neurovascular uncoupling is potentially a major limitation of clinical fMRI, particularly in the setting of mass lesions in the brain such as brain tumors and intracranial vascular malformations that are associated with alterations in regional hemodynamics on either an acquired or congenital basis. As such, breath-hold cerebrovascular reactivity mapping constitutes an essential component of quality control analysis in clinical fMRI, particularly when performed for presurgical mapping of eloquent cortex. Exogenous carbon dioxide challenges used for cerebrovascular reactivity mapping will also be discussed, and their applications to the evaluation of cerebrovascular reserve and cerebrovascular disease will be described.
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Affiliation(s)
- J J Pillai
- From the Division of Neuroradiology (J.J.P.), Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - D J Mikulis
- Department of Medical Imaging (D.J.M.), The University of Toronto, The University Health Network, The Toronto Western Hospital, Toronto, Ontario, Canada
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120
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Cerebrovascular reactivity in the brain white matter: magnitude, temporal characteristics, and age effects. J Cereb Blood Flow Metab 2014; 34:242-7. [PMID: 24192640 PMCID: PMC3915204 DOI: 10.1038/jcbfm.2013.194] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 11/08/2022]
Abstract
White matter (WM) comprises about half of the brain and its dysfunction is implicated in many brain disorders. While structural properties in healthy and diseased WM have been extensively studied, relatively little is known about the physiology underlying these structural characteristics. Recent advances in magnetic resonance (MR) technologies provided new opportunities to better understand perfusion and microvasculature in the WM. Here, we aim to evaluate vasodilatory capacity of the WM vasculature, which is thought to be important in tissue ischemia and autoregulation. Fifteen younger and fifteen older subjects performed a CO2 inhalation task while blood-oxygenation-level-dependent (BOLD) magnetic resonance imaging (MRI) images were continuously collected. The cerebrovascular reactivity (CVR) index showed that the value of CVR in the WM (0.03±0.002%/mm Hg) was positive, but was significantly lower than that in the gray matter (GM) (0.22±0.01%/mm Hg). More strikingly, the WM response showed a temporal delay of 19±3 seconds compared with GM, which was attributed to the longer time it takes for extravascular CO2 to change. With age, WM CVR response becomes greater and faster, which is opposite to the changes seen in the GM. These data suggest that characteristics of WM CVR are different from that of GM and caution should be used when interpreting pathologic WM CVR results.
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121
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Fierstra J, Sobczyk O, Battisti-Charbonney A, Mandell DM, Poublanc J, Crawley AP, Mikulis DJ, Duffin J, Fisher JA. Measuring cerebrovascular reactivity: what stimulus to use? J Physiol 2013; 591:5809-21. [PMID: 24081155 DOI: 10.1113/jphysiol.2013.259150] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Cerebrovascular reactivity is the change in cerebral blood flow in response to a vasodilatory or vasoconstrictive stimulus. Measuring variations of cerebrovascular reactivity between different regions of the brain has the potential to not only advance understanding of how the cerebral vasculature controls the distribution of blood flow but also to detect cerebrovascular pathophysiology. While there are standardized and repeatable methods for estimating the changes in cerebral blood flow in response to a vasoactive stimulus, the same cannot be said for the stimulus itself. Indeed, the wide variety of vasoactive challenges currently employed in these studies impedes comparisons between them. This review therefore critically examines the vasoactive stimuli in current use for their ability to provide a standard repeatable challenge and for the practicality of their implementation. Such challenges include induced reductions in systemic blood pressure, and the administration of vasoactive substances such as acetazolamide and carbon dioxide. We conclude that many of the stimuli in current use do not provide a standard stimulus comparable between individuals and in the same individual over time. We suggest that carbon dioxide is the most suitable vasoactive stimulus. We describe recently developed computer-controlled MRI compatible gas delivery systems which are capable of administering reliable and repeatable vasoactive CO2 stimuli.
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Affiliation(s)
- J Fierstra
- J. Duffin: Department of Physiology, Medical Sciences Building, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S 1A8.
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