Methods for cleaning the BOLD fMRI signal

Available online 9 December 2016 http://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3Dihubhttp://www.sciencedirect.com/science/article/pii/S1053811916307418?via%3DihubBlood oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI) has rapidly become a popular technique for the investigation of brain function in healthy individuals, patients as well as in animal studies. However, the BOLD signal arises from a complex mixture of neuronal, metabolic and vascular processes, being therefore an indirect measure of neuronal activity, which is further severely corrupted by multiple non-neuronal fluctuations of instrumental, physiological or subject-specific origin. This review aims to provide a comprehensive summary of existing methods for cleaning the BOLD fMRI signal. The description is given from a methodological point of view, focusing on the operation of the different techniques in addition to pointing out the advantages and limitations in their application. Since motion-related and physiological noise fluctuations are two of the main noise components of the signal, techniques targeting their removal are primarily addressed, including both data-driven approaches and using external recordings. Data-driven approaches, which are less specific in the assumed model and can simultaneously reduce multiple noise fluctuations, are mainly based on data decomposition techniques such as principal and independent component analysis. Importantly, the usefulness of strategies that benefit from the information available in the phase component of the signal, or in multiple signal echoes is also highlighted. The use of global signal regression for denoising is also addressed. Finally, practical recommendations regarding the optimization of the preprocessing pipeline for the purpose of denoising and future venues of research are indicated. Through the review, we summarize the importance of signal denoising as an essential step in the analysis pipeline of task-based and resting state fMRI studies.This work was supported by the Spanish Ministry of Economy and Competitiveness [Grant PSI 2013–42343 Neuroimagen Multimodal], the Severo Ochoa Programme for Centres/Units of Excellence in R & D [SEV-2015-490], and the research and writing of the paper were supported by the NIMH and NINDS Intramural Research Programs (ZICMH002888) of the NIH/HHS

Closing eyes during auditory memory retrieval modulates alpha rhythm but does not alter tau rhythm

Available online 20 April 2019The alpha power increase that occurs when the eyes are closed is one of the most well-known effects in human electrophysiology. In particular, previous psychological studies have investigated whether eye closure can boost memory performance under certain circumstances, providing contradictory evidence across sensory input modalities. Although alpha power is modulated during different phases of memory and these modulations are correlated with performance, few studies have reported on the relationship between eye closure, memory, and alpha-band power. The present study investigates the influence of eye closure while participants (n = 21) performed an auditory recognition memory task with spoken words during the recording of magnetoencephalography (MEG) data. Our results showed no evidence for a behavioural effect of eye closure in the performance of the task. In addition, electrophysiological responses to the stimuli showed the expected alpha event-related desynchronization (ERD) 0.5–1 s and a high-alpha/beta event-related synchronization (ERS) 1–2 s after word onset. The data showed the expected memory effect, i.e. remembered words elicited greater 10 Hz ERD than forgotten words in the brain regions typically associated with the language network, suggesting a modulation of tau rhythm. Eye closure modulated alpha rhythm only in posterior-parietal and occipital regions. The lack of interaction and the different localizations found for modulations of tau and classical alpha rhythms suggests that these rhythms play distinct functional roles in memory performance.This research was possible thanks to the support of the “Severo Ochoa Program for Centres/Units of Excellence in R&D” (SEV-2015-490). AB was supported by the Basque Government (Eusko Jaurlaritza) under the program “Ikertzaile ez doktoreen doktoretza-aurreko formakuntza programa” ( PRE_2015_2_0208), CCG was supported by the Spanish Ministry of Economy and Competitiveness through the Juan de la Cierva (IJCI- 2014-20821) and Ramon y Cajal (RYC-2017-21845) Fellowships

Effect of prewhitening in resting-state functional near-infrared spectroscopy data

Published: 24 October 2018Near-infrared spectroscopy (NIRS) offers the potential to characterize resting-state functional connectivity (RSFC) in populations that are not easily assessed otherwise, such as young infants. In addition to the advantages of NIRS, one should also consider that the RS-NIRS signal requires specific data preprocessing and analysis. In particular, the RS-NIRS signal shows a colored frequency spectrum, which can be observed as temporal autocorrelation, thereby introducing spurious correlations. To address this issue, prewhitening of the RS-NIRS signal has been recently proposed as a necessary step to remove the signal temporal autocorrelation and therefore reduce false-discovery rates. However, the impact of this step on the analysis of experimental RS-NIRS data has not been thoroughly assessed prior to the present study. Here, the results of a standard preprocessing pipeline in a RS-NIRS dataset acquired in infants are compared with the results after incorporating two different prewhitening algorithms. Our results with a standard preprocessing replicated previous studies. Prewhitening altered RSFC patterns and disrupted the antiphase relationship between oxyhemoglobin and deoxyhemoglobin. We conclude that a better understanding of the effect of prewhitening on RS-NIRS data is still needed before directly considering its incorporation to the standard preprocessing pipeline.This research was possible due to the support of the Basque Government predoctoral grant PRE_2016_2_0188 to Borja Blanco, as well as the support of the Spanish Ministry of Economy and Competitiveness through the project PSI 2014-54512-P, Juan de la Cierva Fellowship (IJCI-2014-20821) and the “Severo Ochoa” Programme for Centres/Units of Excellence in R & D (SEV-2015-490)

A LOW RANK AND SPARSE PARADIGM FREE MAPPING ALGORITHM FOR DECONVOLUTION OF FMRI DATA

Date Added to IEEE Xplore: 25 May 2021Current deconvolution algorithms for functional magnetic resonance imaging (fMRI) data are hindered by widespread signal changes arising from motion or physiological processes (e.g. deep breaths) that can be interpreted incorrectly as neuronal-related hemodynamic events. This work proposes a novel deconvolution approach that simultaneously estimates global signal fluctuations and neuronalrelated activity with no prior information about the timings of the blood oxygenation level-dependent (BOLD) events by means of a low rank plus sparse decomposition algorithm. The performance of the proposed method is evaluated on simulated and experimental fMRI data, and compared with state-of-the-art sparsity-based deconvolution approaches and with a conventional analysis that is aware of the temporal model of the neuronal-related activity. We demonstrate that the novel low-rank and sparse paradigm free mapping algorithm can estimate global signal fluctuations related to motion in our task, while estimating the neuronal-related activity with high fidelity

Phonatory and articulatory representations of speech production in cortical and subcortical fMRI responses

Speaking involves coordination of multiple neuromotor systems, including respiration, phonation and articulation. Developing non-invasive imaging methods to study how the brain controls these systems is critical for understanding the neurobiology of speech production. Recent models and animal research suggest that regions beyond the primary motor cortex (M1) help orchestrate the neuromotor control needed for speaking, including cortical and sub-cortical regions. Using contrasts between speech conditions with controlled respiratory behavior, this fMRI study investigates articulatory gestures involving the tongue, lips and velum (i.e., alveolars versus bilabials, and nasals versus orals), and phonatory gestures (i.e., voiced versus whispered speech). Multivariate pattern analysis (MVPA) was used to decode articulatory gestures in M1, cerebellum and basal ganglia. Furthermore, apart from confirming the role of a mid-M1 region for phonation, we found that a dorsal M1 region, linked to respiratory control, showed significant differences for voiced compared to whispered speech despite matched lung volume observations. This region was also functionally connected to tongue and lip M1 seed regions, underlying its importance in the coordination of speech. Our study confirms and extends current knowledge regarding the neural mechanisms underlying neuromotor speech control, which hold promise to study neural dysfunctions involved in motor-speech disorders non-invasively.Tis work was supported by the Spanish Ministry of Economy and Competitiveness through the Juan de la Cierva Fellowship (FJCI-2015-26814), and the Ramon y Cajal Fellowship (RYC-2017- 21845), the Spanish State Research Agency through the BCBL “Severo Ochoa” excellence accreditation (SEV-2015-490), the Basque Government (BERC 2018- 2021) and the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (No 799554).info:eu-repo/semantics/publishedVersio

Hemodynamic Deconvolution Demystified: Sparsity-Driven Regularization at Work

Deconvolution of the hemodynamic response is an important step to access short timescales of brain activity recorded by functional magnetic resonance imaging (fMRI). Albeit conventional deconvolution algorithms have been around for a long time (e.g., Wiener deconvolution), recent state-of-the-art methods based on sparsity-pursuing regularization are attracting increasing interest to investigate brain dynamics and connectivity with fMRI. This technical note revisits the main concepts underlying two main methods, Paradigm Free Mapping and Total Activation, in the most accessible way. Despite their apparent differences in the formulation, these methods are theoretically equivalent as they represent the synthesis and analysis sides of the same problem, respectively. We demonstrate this equivalence in practice with their best-available implementations using both simulations, with different signal-to-noise ratios, and experimental fMRI data acquired during a motor task and resting-state. We evaluate the parameter settings that lead to equivalent results, and showcase the potential of these algorithms compared to other common approaches. This note is useful for practitioners interested in gaining a better understanding of state-of-the-art hemodynamic deconvolution, and aims to answer questions that practitioners often have regarding the differences between the two methods.Comment: 18 pages, 6 figures, submitted to Apertur

Lag-Optimized Blood Oxygenation Level Dependent Cerebrovascular Reactivity Estimates Derived From Breathing Task Data Have a Stronger Relationship With Baseline Cerebral Blood Flow

Published: 15 June 2022Cerebrovascular reactivity (CVR), an important indicator of cerebrovascular health, is commonly studied with the Blood Oxygenation Level Dependent functional MRI (BOLD-fMRI) response to a vasoactive stimulus. Theoretical and empirical evidence suggests that baseline cerebral blood flow (CBF) modulates BOLD signal amplitude and may influence BOLD-CVR estimates. We address how acquisition and modeling choices affect the relationship between baseline cerebral blood flow (bCBF) and BOLD-CVR: whether BOLD-CVR is modeled with the inclusion of a breathing task, and whether BOLD-CVR amplitudes are optimized for hemodynamic lag effects. We assessed between-subject correlations of average GM values and within-subject spatial correlations across cortical regions. Our results suggest that a breathing task addition to a resting-state acquisition, alongside lag-optimization within BOLD-CVR modeling, can improve BOLD-CVR correlations with bCBF, both between- and within-subjects, likely because these CVR estimates are more physiologically accurate. We report positive correlations between bCBF and BOLD-CVR, both between- and within-subjects. The physiological explanation of this positive correlation is unclear; research with larger samples and tightly controlled vasoactive stimuli is needed. Insights into what drives variability in BOLD-CVR measurements and related measurements of cerebrovascular function are particularly relevant when interpreting results in populations with altered vascular and/or metabolic baselines or impaired cerebrovascular reserve.This work was supported by the Center for Translational Imaging at Northwestern University. The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research was supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health [K12HD073945]. KZ was supported by an NIH-funded training program [T32EB025766]. SM was supported by the European Union’s Horizon 2020 research and innovation program [Marie Skłodowska-Curie grant agreement No. 713673] and a fellowship from La Caixa Foundation [ID 100010434, fellowship code LCF/BQ/IN17/11620063]. CC-G was supported by the Spanish Ministry of Economy and Competitiveness [Ramon y Cajal Fellowship, RYC2017-21845], the Basque Government [BERC 2018-2021 and PIBA_2019_104], and the Spanish Ministry of Science, Innovation and Universities [MICINN; PID2019- 105520GB-100]

A practical modification to a resting state fMRI protocol for improved characterization of cerebrovascular function

Available online 24 June 2021.Cerebrovascular reactivity (CVR), defined here as the Blood Oxygenation Level Dependent (BOLD) response to a CO 2 pressure change, is a useful metric of cerebrovascular function. Both the amplitude and the timing (hemo- dynamic 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 ac- tivity. 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 CO 2 pressure: a breath-hold task to induce hypercapnia (CO 2 increase) and a cued deep breathing task to induce hypocapnia (CO 2 decrease). Our analysis produced voxel-wise estimates of the amplitude (CVR) and timing (lag) of the BOLD-fMRI response to CO 2 by systematically shifting the CO 2 regressor in time to optimize the model fit. This optimization inher- ently 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 CO 2 and BOLD-fMRI signals, and improves our confidence in the plausibility of voxel-wise CVR and hemody- namic 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.This research was supported by the Eunice Kennedy Shriver Na- tional Institute of Child Health and Human Development of the Na- tional Institutes of Health under award number K12HD073945. The pediatric dataset and cerebral palsy dataset were collected with sup- port of National Institutes of Health award R03 HD094615–01A1. The authors would like to acknowledge Marie Wasielewski and Carson Ingo for their support in acquiring these data. K.Z. was supported by an NIH-funded training program (T32EB025766). S.M. was supported by the European Union’s Horizon 2020 research and innovation pro- gram (Marie Sk ł odowska-Curie grant agreement No. 713673), a fel- lowship from La Caixa Foundation (ID 100010434, fellowship code LCF/BQ/IN17/11620063) and C.C.G was supported by the Spanish Ministry of Economy and Competitiveness (Ramon y Cajal Fellowship, RYC-2017- 21845), the Basque Government (BERC 2018–2021 and PIBA_2019_104) and the Spanish Ministry of Science, Innovation and Universities (MICINN; PID2019–105520GB-100)

Quality and denoising in real-time functional magnetic resonance imaging neurofeedback: A methods review

First published: 25 April 2020Neurofeedback training using real-time functional magnetic resonance imaging (rtfMRI-NF) allows subjects voluntary control of localised and distributed brain activity. It has sparked increased interest as a promising non-invasive treatment option in neuropsychiatric and neurocognitive disorders, although its efficacy and clinical significance are yet to be determined. In this work, we present the first extensive review of acquisition, processing and quality control methods available to improve the quality of the neurofeedback signal. Furthermore, we investigate the state of denoising and quality control practices in 128 recently published rtfMRI-NF studies. We found: (a) that less than a third of the studies reported implementing standard real-time fMRI denoising steps, (b) significant room for improvement with regards to methods reporting and (c) the need for methodological studies quantifying and comparing the contribution of denoising steps to the neurofeedback signal quality. Advances in rtfMRI-NF research depend on reproducibility of methods and results. Notably, a systematic effort is needed to build up evidence that disentangles the various mechanisms influencing neurofeedback effects. To this end, we recommend that future rtfMRI-NF studies: (a) report implementation of a set of standard real-time fMRI denoising steps according to a proposed COBIDAS-style checklist (https://osf.io/kjwhf/), (b) ensure the quality of the neurofeedback signal by calculating and reporting community-informed quality metrics and applying offline control checks and (c) strive to adopt transparent principles in the form of methods and data sharing and support of open-source rtfMRI-NF software. Code and data for reproducibility, as well as an interactive environment to explore the study data, can be accessed at https://github. com/jsheunis/quality-and-denoising-in-rtfmri-nf.LSH‐TKI, Grant/Award Number: LSHM16053‐SGF; Philips Researc