Reduction of motion-related artifacts in resting state fMRI using aCompCor.
ABSTRACT: 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.
Project description:"Functional connectivity" techniques are commonplace tools for studying brain organization. A critical element of these analyses is to distinguish variance due to neurobiological signals from variance due to nonneurobiological signals. Multiecho fMRI techniques are a promising means for making such distinctions based on signal decay properties. Here, we report that multiecho fMRI techniques enable excellent removal of certain kinds of artifactual variance, namely, spatially focal artifacts due to motion. By removing these artifacts, multiecho techniques reveal frequent, large-amplitude blood oxygen level-dependent (BOLD) signal changes present across all gray matter that are also linked to motion. These whole-brain BOLD signals could reflect widespread neural processes or other processes, such as alterations in blood partial pressure of carbon dioxide (pCO2) due to ventilation changes. By acquiring multiecho data while monitoring breathing, we demonstrate that whole-brain BOLD signals in the resting state are often caused by changes in breathing that co-occur with head motion. These widespread respiratory fMRI signals cannot be isolated from neurobiological signals by multiecho techniques because they occur via the same BOLD mechanism. Respiratory signals must therefore be removed by some other technique to isolate neurobiological covariance in fMRI time series. Several methods for removing global artifacts are demonstrated and compared, and were found to yield fMRI time series essentially free of motion-related influences. These results identify two kinds of motion-associated fMRI variance, with different physical mechanisms and spatial profiles, each of which strongly and differentially influences functional connectivity patterns. Distance-dependent patterns in covariance are nearly entirely attributable to non-BOLD artifacts.
Project description:Recent resting-state functional connectivity fMRI (RS-fcMRI) research has demonstrated that head motion during fMRI acquisition systematically influences connectivity estimates despite bandpass filtering and nuisance regression, which are intended to reduce such nuisance variability. We provide evidence that the effects of head motion and other nuisance signals are poorly controlled when the fMRI time series are bandpass-filtered but the regressors are unfiltered, resulting in the inadvertent reintroduction of nuisance-related variation into frequencies previously suppressed by the bandpass filter, as well as suboptimal correction for noise signals in the frequencies of interest. This is important because many RS-fcMRI studies, including some focusing on motion-related artifacts, have applied this approach. In two cohorts of individuals (n=117 and 22) who completed resting-state fMRI scans, we found that the bandpass-regress approach consistently overestimated functional connectivity across the brain, typically on the order of r=.10-.35, relative to a simultaneous bandpass filtering and nuisance regression approach. Inflated correlations under the bandpass-regress approach were associated with head motion and cardiac artifacts. Furthermore, distance-related differences in the association of head motion and connectivity estimates were much weaker for the simultaneous filtering approach. We recommend that future RS-fcMRI studies ensure that the frequencies of nuisance regressors and fMRI data match prior to nuisance regression, and we advocate a simultaneous bandpass filtering and nuisance regression strategy that better controls nuisance-related variability.
Project description:Artifactual sources of resting-state (RS) FMRI can originate from head motion, physiology, and hardware. Of these sources, motion has received considerable attention and was found to induce corrupting effects by differentially biasing correlations between regions depending on their distance. Numerous corrective approaches have relied on the identification and censoring of high-motion time points and the use of the brain-wide average time series as a nuisance regressor to which the data are orthogonalized (Global Signal Regression, GSReg). We first replicate the previously reported head-motion bias on correlation coefficients using data generously contributed by Power et al. (2012). We then show that while motion can be the source of artifact in correlations, the distance-dependent bias-taken to be a manifestation of the motion effect on correlation-is exacerbated by the use of GSReg. Put differently, correlation estimates obtained after GSReg are more susceptible to the presence of motion and by extension to the levels of censoring. More generally, the effect of motion on correlation estimates depends on the preprocessing steps leading to the correlation estimate, with certain approaches performing markedly worse than others. For this purpose, we consider various models for RS FMRI preprocessing and show that WMeLOCAL, as subset of the ANATICOR discussed by Jo et al. (2010), denoising approach results in minimal sensitivity to motion and reduces by extension the dependence of correlation results on censoring.
Project description:<h4>Background</h4>Functional neuroimaging research in autism spectrum disorder has reported patterns of decreased long-range, within-network, and interhemispheric connectivity. Research has also reported increased corticostriatal connectivity and between-network connectivity for default and attentional networks. Past studies have excluded individuals with autism and low verbal and cognitive performance (LVCP), so connectivity in individuals more significantly affected with autism has not yet been studied. This represents a critical gap in our understanding of brain function across the autism spectrum.<h4>Methods</h4>Using behavioral support procedures adapted from Nordahl, et al. (J Neurodev Disord 8:20-20, 2016), we completed non-sedated structural and functional MRI scans of 56 children ages 7-17, including LVCP children (<i>n</i>?=?17, mean IQ?=?54), children with autism and higher performance (HVCP, <i>n</i>?=?20, mean IQ?=?106), and neurotypical children (NT, <i>n</i>?=?19, mean IQ?=?111). Preparation included detailed intake questionnaires, video modeling, behavioral and anxiety reduction techniques, active noise-canceling headphones, and in-scan presentation of the Inscapes movie paradigm from Vanderwal et al. (Neuroimage 122:222-32, 2015). A high temporal resolution multiband echoplanar fMRI protocol analyzed motion-free time series data, extracted from concatenated volumes to mitigate the influence of motion artifact. All participants had >?200 volumes of motion-free fMRI scanning. Analyses were corrected for multiple comparisons.<h4>Results</h4>LVCP showed decreased within-network connectivity in default, salience, auditory, and frontoparietal networks (LVCP?<?HVCP) and decreased interhemispheric connectivity (LVCP?<?HVCP=NT). Between-network connectivity was higher for LVCP than NT between default and dorsal attention and frontoparietal networks. Lower IQ was associated with decreased connectivity within the default network and increased connectivity between default and dorsal attention networks.<h4>Conclusions</h4>This study demonstrates that with moderate levels of support, including readily available techniques, information about brain similarities and differences in LVCP individuals can be further studied. This initial study suggested decreased network segmentation and integration in LVCP individuals. Further imaging studies of LVCP individuals with larger samples will add to understanding of origins and effects of autism on brain function and behavior.
Project description:Due to the confounding effects of head motion artifacts on resting-state functional connectivity (RSFC), there has been a growing interest in both acquisition and preprocessing strategies for removing motion-related artifacts from resting state functional Magnetic Resonance Imaging (Rs-fMRI) data. Prospective motion correction by the Siemens' EPI-PACE sequence could offer new insights on the effectiveness of this sequence to correct head motion artifacts in Rs-fMRI data. The head motion parameters along with Rs-fMRI data obtained from 47 healthy individuals scanned with the EPI-PACE sequence is presented in this article. This data is useful to understand the effectiveness of prospective motion correction strategies such as 3D PACE for reducing head motion artifacts in Rs-fMRI data and help devise effective motion correction strategies. The utility of the EPI-PACE sequence in reducing motion correction artifacts in healthy controls can be found in our research article on the topic .
Project description:Whole-brain fMRI signals are a subject of intense interest: variance in the global fMRI signal (the spatial mean of all signals in the brain) indexes subject arousal, and psychiatric conditions such as schizophrenia and autism have been characterized by differences in the global fMRI signal. Further, vigorous debates exist on whether global signals ought to be removed from fMRI data. However, surprisingly little research has focused on the empirical properties of whole-brain fMRI signals. Here we map the spatial and temporal properties of the global signal, individually, in 1000+ fMRI scans. Variance in the global fMRI signal is strongly linked to head motion, to hardware artifacts, and to respiratory patterns and their attendant physiologic changes. Many techniques used to prepare fMRI data for analysis fail to remove these uninteresting kinds of global signal fluctuations. Thus, many studies include, at the time of analysis, prominent global effects of yawns, breathing changes, and head motion, among other signals. Such artifacts will mimic dynamic neural activity and will spuriously alter signal covariance throughout the brain. Methods capable of isolating and removing global artifactual variance while preserving putative "neural" variance are needed; this paper adopts no position on the topic of global signal regression.
Project description:BACKGROUND:Adult attention-deficit/hyperactivity disorder (ADHD) is a serious and frequent psychiatric disorder of multifactorial pathogenesis. Several lines of evidence support the idea that ADHD is, in its core, a disorder of dysfunctional brain connectivity within and between several neurofunctional networks. The primary aim of this study was to investigate associations between the functional connectivity within resting state brain networks and the individual severity of core ADHD symptoms (inattention, hyperactivity, and impulsivity). METHODS:Resting state functional magnetic resonance imaging (rs-fMRI) data of 38 methylphenidate-naïve adults with childhood-onset ADHD (20 women, mean age 40.5?years) were analyzed using independent component analysis (FSL's MELODIC) and FSL's dual regression technique. For motion correction, standard volume-realignment followed by independent component analysis-based automatic removal of motion artifacts (FSL's ICA-AROMA) were employed. To identify well-established brain networks, the independent components found in the ADHD group were correlated with brain networks previously found in healthy participants (Smith et al. PNAS 2009;106:13040-5). To investigate associations between functional connectivity and individual symptom severity, sex, and age, linear regressions were performed. RESULTS:Decomposition of resting state brain activity of adults with ADHD resulted in similar resting state networks as previously described for healthy adults. No significant differences in functional connectivity were seen between women and men. Advanced age was associated with decreased functional connectivity in parts of the bilateral cingulate and paracingulate cortex within the executive control network. More severe hyperactivity was associated with increased functional connectivity in the left putamen, right caudate nucleus, right central operculum and a portion of the right postcentral gyrus within the auditory/sensorimotor network. CONCLUSIONS:The present study supports and extends our knowledge on the involvement of the striatum in the pathophysiology of ADHD, in particular, in the pathogenesis of hyperactivity. Our results emphasize the usefulness of dimensional analyses in the study of ADHD, a highly heterogeneous disorder. TRIAL REGISTRATION:ISRCTN12722296 ( https://doi.org/10.1186/ISRCTN12722296 ).
Project description:Recent fMRI studies have shown fusion of visual motion and disparity signals for shape perception (Ban et al., 2012), and unmasking camouflaged surfaces (Rokers et al., 2009), but no such interaction is known for typical dorsal motion pathway tasks, like grasping and navigation. Here, we investigate human speed perception of forward motion and its representation in the human motion network. We observe strong interaction in medial (V3ab, V6) and lateral motion areas (MT(+)), which differ significantly. Whereas the retinal disparity dominates the binocular contribution to the BOLD activity in the anterior part of area MT(+), headcentric disparity modulation of the BOLD response dominates in area V3ab and V6. This suggests that medial motion areas not only represent rotational speed of the head (Arnoldussen et al., 2011), but also translational speed of the head relative to the scene. Interestingly, a strong response to vergence eye movements was found in area V1, which showed a dependency on visual direction, just like vertical-size disparity. This is the first report of a vertical-size disparity correlate in human striate cortex.
Project description:Functional connectivity analysis of resting-state fMRI data has recently become one of the most common approaches to characterizing individual brain function. It has been widely suggested that the functional connectivity matrix is a useful approximate representation of the brain's connectivity, potentially providing behaviorally or clinically relevant markers. However, functional connectivity estimates are known to be detrimentally affected by various artifacts, including those due to in-scanner head motion. Moreover, as individual functional connections generally covary only very weakly with head motion estimates, motion influence is difficult to quantify robustly, and prone to be neglected in practice. Although the use of individual estimates of head motion, or group-level correlation of motion and functional connectivity has been suggested, a sufficiently sensitive measure of individual functional connectivity quality has not yet been established. We propose a new intuitive summary index, Typicality of Functional Connectivity, to capture deviations from standard brain functional connectivity patterns. In a resting-state fMRI dataset of 245 healthy subjects, this measure was significantly correlated with individual head motion metrics. The results were further robustly reproduced across atlas granularity, preprocessing options, and other datasets, including 1,081 subjects from the Human Connectome Project. In principle, Typicality of Functional Connectivity should be sensitive also to other types of artifacts, processing errors, and possibly also brain pathology, allowing extensive use in data quality screening and quantification in functional connectivity studies as well as methodological investigations.
Project description:There is strong interest in investigating both functional connectivity (FC) using functional magnetic resonance imaging (fMRI) and structural connectivity (SC) using diffusion tensor imaging (DTI). There is also emerging evidence of correspondence between functional and structural pathways within many networks (Greicius, et al., 2009; Skudlarski et al., 2008; van den Heuvel et al., 2009), although some regions without SC exhibit strong FC (Honey et al., 2008). These findings suggest that FC may be mediated by (direct or indirect) anatomical connections, offering an opportunity to supplement fMRI data with DTI data when determining FC. We develop a novel statistical method for determining FC, called anatomically weighted FC (awFC), which combines fMRI and DTI data. Our awFC approach implements a hierarchical clustering algorithm that establishes neural processing networks using a new distance measure consisting of two components, a primary functional component that captures correlations between fMRI signals from different regions and a secondary anatomical weight reflecting probabilities of SC. The awFC approach defaults to conventional unweighted clustering for specific parameter settings. We optimize awFC parameters using a strictly functional criterion, therefore our approach will generally perform at least as well as an unweighted analysis, with respect to intracluster coherence or autocorrelation. AwFC also yields more informative results since it provides structural properties associated with identified functional networks. We apply awFC to two fMRI data sets: resting-state data from 6 healthy subjects and data from 17 subjects performing an auditory task. In these examples, awFC leads to more highly autocorrelated networks than a conventional analysis. We also conduct a simulation study, which demonstrates accurate performance of awFC and confirms that awFC generally yields comparable, if not superior, accuracy relative to a standard approach.