A whole-brain modeling approach to identify individual and group variations in functional connectivity

Resting-state functional connectivity is an important and widely used measure of individual and group differences. Yet, extant statistical methods are limited to linking covariates with variations in functional connectivity across subjects, especially at the voxel-wise level of the whole brain. This paper introduces a modeling approach that regresses whole-brain functional connectivity on covariates. Our approach is a mesoscale approach that enables identification of brain subnetworks. These subnetworks are composite of spatially independent components discovered by a dimension reduction approach (such as whole-brain group ICA) and covariate-related projections determined by the covariate-assisted principal regression, a recently introduced covariance matrix regression method. We demonstrate the efficacy of this approach using a resting-state fMRI dataset of a medium-sized cohort of subjects obtained from the Human Connectome Project. The results suggest that the approach may improve statistical power in detecting interaction effects of gender and alcohol on whole-brain functional connectivity, and in identifying the brain areas contributing significantly to the covariate-related differences in functional connectivity.

Machine learning to predict transplant outcomes: helpful or hype? A national cohort study

An increasing number of studies claim machine learning (ML) predicts transplant outcomes more accurately. However, these claims were possibly confounded by other factors, namely, supplying new variables to ML models. To better understand the prospects of ML in transplantation, we compared ML to conventional regression in a "common" analytic task: predicting kidney transplant outcomes using national registry data. We studied 133 431 adult deceased-donor kidney transplant recipients between 2005 and 2017. Transplant centers were randomly divided into 70% training set (190 centers/97 787 recipients) and 30% validation set (82 centers/35 644 recipients). Using the training set, we performed regression and ML procedures [gradient boosting (GB) and random forests (RF)] to predict delayed graft function, one-year acute rejection, death-censored graft failure C, all-cause graft failure, and death. Their performances were compared on the validation set using -statistics. In predicting rejection, regression (C = 0.601 0.6110.621 ) actually outperformed GB (C = 0.581 0.5910.601 ) and RF (C = 0.569 0.5790.589 ). For all other outcomes, the C-statistics were nearly identical across methods (delayed graft function, 0.717-0.723; death-censored graft failure, 0.637-0.642; all-cause graft failure, 0.633-0.635; and death, 0.705-0.708). Given its shortcomings in model interpretability and hypothesis testing, ML is advantageous only when it clearly outperforms conventional regression; in the case of transplant outcomes prediction, ML seems more hype than helpful.

Developmental score of the infant brain: characterizing diffusion MRI in term- and preterm-born infants

Large-scale longitudinal neuroimaging studies of the infant brain allow us to map the spatiotemporal development of the brain in its early phase. While the postmenstrual age (PMA) is commonly used as a time index to analyze longitudinal MRI data, the nonlinear relationship between PMA and MRI data imposes challenges for downstream analyses. We propose a mathematical model that provides a Developmental Score (DevS) as a data-driven time index to characterize the brain development based on MRI features. 319 diffusion tensor imaging (DTI) datasets were collected from 87 term-born and 66 preterm-born infants at multiple visits, which were automatically segmented based on the JHU neonatal atlas. The mean diffusivity (MD) and fractional anisotropy (FA) in 126 brain parcels were used in the model to derive DevS. We demonstrate that transforming the time index from PMA to DevS improves the linearity of the longitudinal changes in MD and FA in both gray and white matter structures. More importantly, regional developmental differences in DTI metrics between preterm- and term-born infants were identified more clearly using DevS, e.g. 79 structures showed significantly different regression patterns in MD between preterm- and term-born infants, compared to only 27 structures that showed group differences using PMA as the index. Therefore, the DevS model facilitates linear analyses of DTI metrics in the infant brain, and provides a useful tool to characterize altered brain development due to preterm-birth.

Multimodal neuroimaging data integration and pathway analysis

With advancements in technology, the collection of multiple types of measurements on a common set of subjects is becoming routine in science. Some notable examples include multimodal neuroimaging studies for the simultaneous investigation of brain structure and function and multi-omics studies for combining genetic and genomic information. Integrative analysis of multimodal data allows scientists to interrogate new mechanistic questions. However, the data collection and generation of integrative hypotheses is outpacing available methodology for joint analysis of multimodal measurements. In this article, we study high-dimensional multimodal data integration in the context of mediation analysis. We aim to understand the roles that different data modalities play as possible mediators in the pathway between an exposure variable and an outcome. We propose a mediation model framework with two data types serving as separate sets of mediators and develop a penalized optimization approach for parameter estimation. We study both the theoretical properties of the estimator through an asymptotic analysis and its finite-sample performance through simulations. We illustrate our method with a multimodal brain pathway analysis having both structural and functional connectivity as mediators in the association between sex and language processing.

Learning of skilled movements via imitation in ASD

Autism spectrum disorder (ASD) consists of altered performance of a range of skills, including social/communicative and motor skills. It is unclear whether this altered performance results from atypical acquisition or learning of the skills or from atypical "online" performance of the skills. Atypicalities of skilled actions that require both motor and cognitive resources, such as abnormal gesturing, are highly prevalent in ASD and are easier to study in a laboratory context than are social/communicative skills. Imitation has long been known to be impaired in ASD; because learning via imitation is a prime method by which humans acquire skills, we tested the hypothesis that children with ASD show alterations in learning novel gestures via imitation. Eighteen participants with ASD and IQ > 80, ages 8-12.9 years, and 19 typically developing peers performed a task in which they watched a video of a model performing a novel, meaningless arm/hand gesture and copied the gesture. Each gesture video/copy sequence was repeated 4-6 times. Eight gestures were analyzed. Examination of learning trajectories revealed that while children with ASD made nearly as much progress in learning from repetition 1 to repetition 4, the shape of the learning curves differed. Causal modeling demonstrated the shape of the learning curve influenced both the performance of overlearned gestures and autism severity, suggesting that it is in the index of learning mechanisms relevant both to motor skills and to autism core features. Autism Res 2020, 13: 777-784.. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Imitation is a route by which humans learn a wide range of skills, naturally and in therapies. Imitation is known to be altered in autism spectrum disorder (ASD), but learning via imitation has not been rigorously examined. We found that the shape of the learning curve is altered in ASD, in a way that has a significant impact both on measures of autism severity and of other motor skills.

Covariate Assisted Principal regression for covariance matrix outcomes

In this study, we consider the problem of regressing covariance matrices on associated covariates. Our goal is to use covariates to explain variation in covariance matrices across units. As such, we introduce Covariate Assisted Principal (CAP) regression, an optimization-based method for identifying components associated with the covariates using a generalized linear model approach. We develop computationally efficient algorithms to jointly search for common linear projections of the covariance matrices, as well as the regression coefficients. Under the assumption that all the covariance matrices share identical eigencomponents, we establish the asymptotic properties. In simulation studies, our CAP method shows higher accuracy and robustness in coefficient estimation over competing methods. In an example resting-state functional magnetic resonance imaging study of healthy adults, CAP identifies human brain network changes associated with subject demographics.

Template Independent Component Analysis: Targeted and Reliable Estimation of Subject-level Brain Networks using Big Data Population Priors

Large brain imaging databases contain a wealth of information on brain organization in the populations they target, and on individual variability. While such databases have been used to study group-level features of populations directly, they are currently underutilized as a resource to inform single-subject analysis. Here, we propose leveraging the information contained in large functional magnetic resonance imaging (fMRI) databases by establishing population priors to employ in an empirical Bayesian framework. We focus on estimation of brain networks as source signals in independent component analysis (ICA). We formulate a hierarchical "template" ICA model where source signals-including known population brain networks and subject-specific signals-are represented as latent variables. For estimation, we derive an expectation maximization (EM) algorithm having an explicit solution. However, as this solution is computationally intractable, we also consider an approximate subspace algorithm and a faster two-stage approach. Through extensive simulation studies, we assess performance of both methods and compare with dual regression, a popular but ad-hoc method. The two proposed algorithms have similar performance, and both dramatically outperform dual regression. We also conduct a reliability study utilizing the Human Connectome Project and find that template ICA achieves substantially better performance than dual regression, achieving 75-250% higher intra-subject reliability.

Neuroconductor: an R platform for medical imaging analysis

Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience.

High-dimensional multivariate mediation with application to neuroimaging data

Mediation analysis is an important tool in the behavioral sciences for investigating the role of intermediate variables that lie in the path between a treatment and an outcome variable. The influence of the intermediate variable on the outcome is often explored using a linear structural equation model (LSEM), with model coefficients interpreted as possible effects. While there has been significant research on the topic, little work has been done when the intermediate variable (mediator) is a high-dimensional vector. In this work, we introduce a novel method for identifying potential mediators in this setting called the directions of mediation (DMs). DMs linearly combine potential mediators into a smaller number of orthogonal components, with components ranked based on the proportion of the LSEM likelihood each accounts for. This method is well suited for cases when many potential mediators are measured. Examples of high-dimensional potential mediators are brain images composed of hundreds of thousands of voxels, genetic variation measured at millions of single nucleotide polymorphisms (SNPs), or vectors of thousands of variables in large-scale epidemiological studies. We demonstrate the method using a functional magnetic resonance imaging study of thermal pain where we are interested in determining which brain locations mediate the relationship between the application of a thermal stimulus and self-reported pain.

Improved state change estimation in dynamic functional connectivity using hidden semi-Markov models

The study of functional brain networks has grown rapidly over the past decade. While most functional connectivity (FC) analyses estimate one static network structure for the entire length of the functional magnetic resonance imaging (fMRI) time series, recently there has been increased interest in studying time-varying changes in FC. Hidden Markov models (HMMs) have proven to be a useful modeling approach for discovering repeating graphs of interacting brain regions (brain states). However, a limitation lies in HMMs assuming that the sojourn time, the number of consecutive time points in a state, is geometrically distributed. This may encourage inaccurate estimation of the time spent in a state before switching to another state. We propose a hidden semi-Markov model (HSMM) approach for inferring time-varying brain networks from fMRI data, which explicitly models the sojourn distribution. Specifically, we propose using HSMMs to find each subject's most probable series of network states and the graphs associated with each state, while properly estimating and modeling the sojourn distribution for each state. We perform a simulation study, as well as an analysis on both task-based fMRI data from an anxiety-inducing experiment and resting-state fMRI data from the Human Connectome Project. Our results demonstrate the importance of model choice when estimating sojourn times and reveal their potential for understanding healthy and diseased brain mechanisms.

Modular preprocessing pipelines can reintroduce artifacts into fMRI data

The preprocessing pipelines typically used in both task and resting-state functional magnetic resonance imaging (rs-fMRI) analysis are modular in nature: They are composed of a number of separate filtering/regression steps, including removal of head motion covariates and band-pass filtering, performed sequentially and in a flexible order. In this article, we illustrate the shortcomings of this approach, as we show how later preprocessing steps can reintroduce artifacts previously removed from the data in prior preprocessing steps. We show that each regression step is a geometric projection of data onto a subspace, and that performing a sequence of projections can move the data into subspaces no longer orthogonal to those previously removed, reintroducing signal related to nuisance covariates. Thus, linear filtering operations are not commutative, and the order in which the preprocessing steps are performed is critical. These issues can arise in practice when any combination of standard preprocessing steps including motion regression, scrubbing, component-based correction, physiological correction, global signal regression, and temporal filtering are performed sequentially. In this work, we focus primarily on rs-fMRI. We illustrate the problem both theoretically and empirically through application to a test-retest rs-fMRI data set, and suggest remedies. These include (a) combining all steps into a single linear filter, or (b) sequential orthogonalization of covariates/linear filters performed in series.

Mixed effect machine learning: A framework for predicting longitudinal change in hemoglobin A1c

Accurate and reliable prediction of clinical progression over time has the potential to improve the outcomes of chronic disease. The classical approach to analyzing longitudinal data is to use (generalized) linear mixed-effect models (GLMM). However, linear parametric models are predicated on assumptions, which are often difficult to verify. In contrast, data-driven machine learning methods can be applied to derive insight from the raw data without a priori assumptions. However, the underlying theory of most machine learning algorithms assume that the data is independent and identically distributed, making them inefficient for longitudinal supervised learning. In this study, we formulate an analytic framework, which integrates the random-effects structure of GLMM into non-linear machine learning models capable of exploiting temporal heterogeneous effects, sparse and varying-length patient characteristics inherent in longitudinal data. We applied the derived mixed-effect machine learning (MEml) framework to predict longitudinal change in glycemic control measured by hemoglobin A1c (HbA1c) among well controlled adults with type 2 diabetes. Results show that MEml is competitive with traditional GLMM, but substantially outperformed standard machine learning models that do not account for random-effects. Specifically, the accuracy of MEml in predicting glycemic change at the 1st, 2nd, 3rd, and 4th clinical visits in advanced was 1.04, 1.08, 1.11, and 1.14 times that of the gradient boosted model respectively, with similar results for the other methods. To further demonstrate the general applicability of MEml, a series of experiments were performed using real publicly available and synthetic data sets for accuracy and robustness. These experiments reinforced the superiority of MEml over the other methods. Overall, results from this study highlight the importance of modeling random-effects in machine learning approaches based on longitudinal data. Our MEml method is highly resistant to correlated data, readily accounts for random-effects, and predicts change of a longitudinal clinical outcome in real-world clinical settings with high accuracy.

Improved estimation of subject-level functional connectivity using full and partial correlation with empirical Bayes shrinkage

Reliability of subject-level resting-state functional connectivity (FC) is determined in part by the statistical techniques employed in its estimation. Methods that pool information across subjects to inform estimation of subject-level effects (e.g., Bayesian approaches) have been shown to enhance reliability of subject-level FC. However, fully Bayesian approaches are computationally demanding, while empirical Bayesian approaches typically rely on using repeated measures to estimate the variance components in the model. Here, we avoid the need for repeated measures by proposing a novel measurement error model for FC describing the different sources of variance and error, which we use to perform empirical Bayes shrinkage of subject-level FC towards the group average. In addition, since the traditional intra-class correlation coefficient (ICC) is inappropriate for biased estimates, we propose a new reliability measure denoted the mean squared error intra-class correlation coefficient (ICCMSE) to properly assess the reliability of the resulting (biased) estimates. We apply the proposed techniques to test-retest resting-state fMRI data on 461 subjects from the Human Connectome Project to estimate connectivity between 100 regions identified through independent components analysis (ICA). We consider both correlation and partial correlation as the measure of FC and assess the benefit of shrinkage for each measure, as well as the effects of scan duration. We find that shrinkage estimates of subject-level FC exhibit substantially greater reliability than traditional estimates across various scan durations, even for the most reliable connections and regardless of connectivity measure. Additionally, we find partial correlation reliability to be highly sensitive to the choice of penalty term, and to be generally worse than that of full correlations except for certain connections and a narrow range of penalty values. This suggests that the penalty needs to be chosen carefully when using partial correlations.

Decoupling of reaction time-related default mode network activity with cognitive demand

Reaction Time (RT) is associated with increased amplitude of the Blood Oxygen-Level Dependent (BOLD) response in task positive regions. Few studies have focused on whether opposing RT-related suppression of task activity also occurs. The current study used two Go/No-go tasks with different cognitive demands to examine regions that showed greater BOLD suppression for longer RT trials. These RT-related suppression effects occurred within the DMN and were task-specific, localizing to separate regions for the two tasks. In the task requiring working memory, RT-related de-coupling of the DMN occurred. This was reflected by opposing RT-BOLD effects for different DMN regions, as well as by reduced positive RT-related Psycho-Physiological Interaction (PPI) connectivity within the DMN and a lack of negative RT-related PPI connectivity between DMN and task positive regions. The results suggest that RT-related DMN suppression is task-specific. RT-related de-coupling of the DMN with more complex task demands may contribute to lapses of attention and performance decrements that occur during cognitively-demanding tasks.

Parallel group independent component analysis for massive fMRI data sets

Independent component analysis (ICA) is widely used in the field of functional neuroimaging to decompose data into spatio-temporal patterns of co-activation. In particular, ICA has found wide usage in the analysis of resting state fMRI (rs-fMRI) data. Recently, a number of large-scale data sets have become publicly available that consist of rs-fMRI scans from thousands of subjects. As a result, efficient ICA algorithms that scale well to the increased number of subjects are required. To address this problem, we propose a two-stage likelihood-based algorithm for performing group ICA, which we denote Parallel Group Independent Component Analysis (PGICA). By utilizing the sequential nature of the algorithm and parallel computing techniques, we are able to efficiently analyze data sets from large numbers of subjects. We illustrate the efficacy of PGICA, which has been implemented in R and is freely available through the Comprehensive R Archive Network, through simulation studies and application to rs-fMRI data from two large multi-subject data sets, consisting of 301 and 779 subjects respectively.

Neural Correlates of Visuomotor Learning in Autism

Motor impairments are prevalent in children with autism spectrum disorder. The Serial Reaction Time Task, a well-established visuomotor sequence learning probe, has produced inconsistent behavioral findings in individuals with autism. Moreover, it remains unclear how underlying neural processes for visuomotor learning in children with autism compare to processes for typically developing children. Neural activity differences were assessed using functional magnetic resonance imaging during a modified version of the Serial Reaction Time Task in children with and without autism. Though there was no group difference in visuomotor sequence learning, underlying patterns of neural activation significantly differed when comparing sequence (i.e., learning) to random (i.e., nonlearning) blocks. Children with autism demonstrated decreased activity in brain regions implicated in visuomotor sequence learning: superior temporal sulcus and posterior cingulate cortex. The findings implicate differences in brain mechanisms that support initial sequence learning in autism and can help explain behavioral observations of autism-associated impairments in skill development (motor, social, communicative) reliant on visuomotor integration.

A Phase 1 Randomized, Blinded Comparison of the Pharmacokinetics and Colonic Distribution of Three Candidate Rectal Microbicide Formulations of Tenofovir 1% Gel with Simulated Unprotected Sex (CHARM-02)

CHARM-02 is a crossover, double-blind, randomized trial to compare the safety and pharmacokinetics of three rectally applied tenofovir 1% gel candidate rectal microbicides of varying osmolalities: vaginal formulation (VF) (3111 mOsmol/kg), the reduced glycerin vaginal formulation (RGVF) (836 mOsmol/kg), and an isoosmolal rectal-specific formulation (RF) (479 mOsmol/kg). Participants (n = 9) received a single, 4 ml, radiolabeled dose of each gel twice, once with and once without simulated unprotected receptive anal intercourse (RAI). The safety, plasma tenofovir pharmacokinetics, colonic small molecule permeability, and SPECT/CT imaging of lower gastrointestinal distribution of drug and virus surrogate were assessed. There were no Grade 3 or 4 adverse events reported for any of the products. Overall, there were more Grade 2 adverse events in the VF group compared to RF (p = 0.006) and RGVF (p = 0.048). In the absence of simulated unprotected RAI, VF had up to 3.8-fold greater systemic tenofovir exposure, 26- to 234-fold higher colonic permeability of the drug surrogate, and 1.5- to 2-fold greater proximal migration in the colonic lumen, when compared to RF and RGVF. Similar trends were observed with simulated unprotected RAI, but most did not reach statistical significance. SPECT analysis showed 86% (standard deviation 19%) of the drug surrogate colocalized with the virus surrogate in the colonic lumen. There were no significant differences between the RGVF and RF formulation, with the exception of a higher plasma tenofovir concentration of RGVF in the absence of simulated unprotected RAI. VF had the most adverse events, highest plasma tenofovir concentrations, greater mucosal permeability of the drug surrogate, and most proximal colonic luminal migration compared to RF and RGVF formulations. There were no major differences between RF and RGVF formulations. Simultaneous assessment of toxicity, systemic and luminal pharmacokinetics, and colocalization of drug and viral surrogates substantially informs rectal microbicide product development.

Reproducibility and Temporal Structure in Weekly Resting-State fMRI over a Period of 3.5 Years

Resting-state functional MRI (rs-fMRI) permits study of the brain’s functional networks without requiring participants to perform tasks. Robust changes in such resting state networks (RSNs) have been observed in neurologic disorders, and rs-fMRI outcome measures are candidate biomarkers for monitoring clinical trials, including trials of extended therapeutic interventions for rehabilitation of patients with chronic conditions. In this study, we aim to present a unique longitudinal dataset reporting on a healthy adult subject scanned weekly over 3.5 years and identify rs-fMRI outcome measures appropriate for clinical trials. Accordingly, we assessed the reproducibility, and characterized the temporal structure of, rs-fMRI outcome measures derived using independent component analysis (ICA). Data was compared to a 21-person dataset acquired on the same scanner in order to confirm that the values of the single-subject RSN measures were within the expected range as assessed from the multi-participant dataset. Fourteen RSNs were identified, and the inter-session reproducibility of outcome measures—network spatial map, temporal signal fluctuation magnitude, and between-network connectivity (BNC)–was high, with executive RSNs showing the highest reproducibility. Analysis of the weekly outcome measures also showed that many rs-fMRI outcome measures had a significant linear trend, annual periodicity, and persistence. Such temporal structure was most prominent in spatial map similarity, and least prominent in BNC. High reproducibility supports the candidacy of rs-fMRI outcome measures as biomarkers, but the presence of significant temporal structure needs to be taken into account when such outcome measures are considered as biomarkers for rehabilitation-style therapeutic interventions in chronic conditions.

Estimating a graphical intra-class correlation coefficient (GICC) using multivariate probit-linear mixed models

Data reproducibility is a critical issue in all scientific experiments. In this manuscript, the problem of quantifying the reproducibility of graphical measurements is considered. The image intra-class correlation coefficient (I2C2) is generalized and the graphical intra-class correlation coefficient (GICC) is proposed for such purpose. The concept for GICC is based on multivariate probit-linear mixed effect models. A Markov Chain Monte Carlo EM (mcm-cEM) algorithm is used for estimating the GICC. Simulation results with varied settings are demonstrated and our method is applied to the KIRBY21 test-retest dataset.

Resting brain activity in disorders of consciousness: a systematic review and meta-analysis

OBJECTIVE

To quantitatively synthesize results from neuroimaging studies that evaluated patterns of resting functional activity in patients with disorders of consciousness (DOC).

METHODS

We performed a systematic review and coordinate-based meta-analysis of studies published up to May 2014. Studies were included if they compared resting-state functional neuroimaging data acquired in patients with DOC (coma, minimally conscious state, emergence from minimally conscious state, or vegetative state) with a group of healthy controls. Coordinate-based meta-analysis was performed in studies that included voxel-based comparisons at the whole-brain level and if analysis was accomplished with data-driven approaches.

RESULTS

A total of 36 studies (687 patients, 637 healthy controls) were included in the systematic review. Reported DOC were vegetative state (43.2%), coma (23.4%), minimally conscious state (22.8%), and emergence from minimally conscious state (1.6%); the most common etiologies of DOC were traumatic brain injury (37.7%) and anoxic brain injury (36.9%). Functional neuroimaging was accomplished using fMRI (16 studies), PET (15 studies), SPECT (4 studies), and both PET and SPECT in one study. Meta-analysis in 13 studies (272 patients, 259 healthy controls) revealed consistently reduced activity in patients with DOC in bilateral medial dorsal nucleus of the thalamus, left cingulate, posterior cingulate, precuneus, and middle frontal and medial temporal gyri.

CONCLUSIONS

In patients with DOC evaluated in the resting state, functional neuroimaging indicates markedly reduced activity within midline cortical and subcortical sites, anatomical structures that have been linked to the default-mode network. Studies are needed to determine the relation between activation (and coherence) within these structures and the emergence of conscious awareness.

Reduction of motion-related artifacts in resting state fMRI using aCompCor

Recent studies have illustrated that motion-related artifacts remain in resting-state fMRI (rs-fMRI) data even after common corrective processing procedures have been applied, but the extent to which head motion distorts the data may be modulated by the corrective approach taken. We compare two different methods for estimating nuisance signals from tissues not expected to exhibit BOLD fMRI signals of neuronal origin: 1) the more commonly used mean signal method and 2) the principal components analysis approach (aCompCor: Behzadi et al., 2007). Further, we investigate the added benefit of "scrubbing" (Power et al., 2012) following both methods. We demonstrate that the use of aCompCor removes motion artifacts more effectively than tissue-mean signal regression. In addition, inclusion of more components from anatomically defined regions of no interest better mitigates motion-related artifacts and improves the specificity of functional connectivity estimates. While scrubbing further attenuates motion-related artifacts when mean signals are used, scrubbing provides no additional benefit in terms of motion artifact reduction or connectivity specificity when using aCompCor.