Single timecourses in a single subject demonstrate a relationship between head motion and changes in the BOLD signal, even after data realignment and regression of realignment estimates and their derivatives from the data. shows rs-fcMRI timecourses at 3 left occipital regions of interest (ROIs) in a single subject. These data are from a single child with RMS movement of 0.50 mm (processed data are 3 mm isotropic voxels derived from 3.75 × 3.75 × 4 mm acquisition voxels). The extent of movement in this scan would be considered low (i.e., of high quality) by many investigators. The timecourses are all quite similar, and there are several major peaks and troughs in the data. displays the six head realignment estimates for this subject. shows the absolute values of the differentials of the timecourses, identifying the periods in which the rs-fcMRI signal was most rapidly changing. These periods correspond to the peaks and troughs of , and compresses the six realignment parameters into a single index of framewise displacement (FD) by summing the absolute values of the differentials of the six parameters. There is evident correspondence between plots in . As Figure S2
shows, such relationships between timecourses and head displacement are not unique to occipital cortex, and can be seen throughout the brain. The pattern is quite similar across ROIs, but there are differences in the sensitivity of particular timecourses to particular movements, which might result from the proximity of ROIs to gray/white matter or gray matter/CSF interfaces in particular directions.
Frame-by-frame changes in rs-fcMRI signal are related to frame-by-frame changes in head position even after motion regression
A general relationship between head motion and changes in BOLD signal across the brain can be seen in every subject examined in this paper (N=119 in four cohorts). A brain-wide collection of 264 ROIs based upon meta-analytic fMRI data and resting state functional connectivity data (independent of the present data) (Power et al., in press
) was used to produce rs-fcMRI timecourses in each subject (see Methods, Table S1
for coordinates, Figure S3
for locations on a brain surface). plots the absolute values of the derivatives of the 264 timecourses as a function of framewise displacement for the same subject shown in . A loess curve using a quadratic fit over the adjacent 5000 data points is shown in black. The data are scattered, but there is an unmistakable trend for frames with high movement to be frames with large changes in many timecourses. plots such loess curves for all 22 children in Cohort 1, demonstrating that this trend is a general feature of the data, and is not particular to any subject. As the inset shows, there is a strong relationship of motion and rs-fcMRI signal change down to a framewise displacement of 0, suggesting that any and all movement tends to increase the amplitude of rs-fcMRI signal changes.
Frame-by-frame head displacement is related to frame-by-frame changes in rs-fcMRI signal throughout the brain and across subjects
It is now clear that across subjects, periods of head movement tend to contain rs-fcMRI data in which BOLD signal is rapidly and substantially changing. Neural activity representing movement planning and execution is surely present at such times, but the signal changes observed during movement do not correspond to the neuroanatomical patterns one would predict for motor-related neural activity. For example, as Figure S4
shows, during head motion, signal changes are not confined to primary motor, pre-motor, or supplementary motor regions, but are instead found throughout the entire brain. Moreover, the amplitude of these signal excursions are often very large - far greater than the signal changes produced by typical motor tasks (e.g., button-pushing or speaking). It is therefore unlikely that these signal changes reflect motor-related neural activity to any great extent. Instead, it is far more likely that movement disrupts magnetic gradient establishment or BOLD signal readout (Hutton et al., 2002
), that many slices or entire volumes of data have been contaminated with artifact during periods of movement, and that this contamination has not been completely removed by fMRI preprocessing and functional connectivity processing. In fMRI studies, such noise in single subjects is dampened through trial averaging. This averaging is impossible in rs-fcMRI studies, which depend upon covariance estimated in long timecourses. If large-amplitude changes contaminate rs-fcMRI timecourses, they will alter patterns of covariance according to their prevalence, magnitude, and spatial distribution, and could lead to distorted estimates of rs-fcMRI correlation between brain regions.
Given the presence of motion-related artifact in the data, how might one detect and/or minimize its impact? All functional connectivity processing streams involve some method of “artifact removal” that is aimed to reduce such artifacts. One approach to removing or minimizing motion-related effects has been to use head realignment parameters or other motion estimates as nuisance regressors, and to attempt to regress movement effects from the data (e.g., (Fox et al., 2006
; Fox et al., 2005
; Fox et al., 2009
; Weissenbacher et al., 2009
)). However, the data presented thus far have already undergone such a procedure, and subsequent figures will show how regression neither causes the effects shown here, nor is it capable of completely removing the effects shown here. This may be because there is not a strong, simple, linear relationship between movement estimates and changes in the BOLD signal throughout the brain, or because the regressions used here were not tailored to every voxel’s displacement. Another approach is to use covariance-based approaches such as component analysis (e.g. ICA, implemented in software packages such as MELODIC or GIFT) to identify and remove “artifactual” components in the data (e.g., (Beckmann and Smith, 2004
; Erhardt et al., 2010
; Robinson et al., 2009a
)). Although some artifactual signals (e.g. “ringing”) are easily identified and removed using such procedures, other artifactual signals may be more ambiguous, and decisions about retaining or discarding such components are somewhat subjective. Since regressions do not fully remove motion-related signal, and because component removal entails subjective decisions about what constitutes artifact, we adopt a different approach, described below.
Head motion tends to occur sporadically in cooperative subjects. Thus, motion-induced signal changes tend to behave as burst noise. Rather than attempting to parse “true” from “artifactual” signal within all frames, we propose to identify and entirely eliminate frames of suspect quality from our rs-fcMRI analyses to detect and characterize motion-related artifact. Previous studies that have examined the concatenation of discontinuous rs-fcMRI data have found no deleterious effects upon functional connectivity (Fair et al., 2007
; Van Dijk et al., 2010
), and similar “temporal masking” approaches have been used in other rs-fcMRI studies (e.g. (Barnes et al., 2011
; Fransson et al., 2007
; Jones et al., 2010
; Kennedy and Courchesne, 2008
; Smyser et al., 2010
; Smyser et al., 2011
)) and in task fMRI (e.g., (Birn et al., 2004
)). Generally, we propose two indices of data quality that can be used to flag frames of suspect quality, creating temporal masks of the data. These temporal masks can be augmented and combined in various ways to produce a final temporal mask, which specifies frames to ignore when performing calculations upon the data (similar approaches using frame elimination or weighting could be implemented in AFNI or SPM’s ArtRepair). We refer to this process as “scrubbing”.
Specifically, we begin our procedure after functional connectivity processing has finished, because bandpassing, often an integral part of functional connectivity processing, cannot be performed properly upon temporally discontinuous data. The first framewise data quality index is framewise displacement (e.g., ), calculated as the sum of the absolute values of the derivatives of the six realignment parameters. Framewise displacement thus measures how much the head changed position from one frame to the next. show framewise displacement values for two subjects (see Figure S5
for further examples). The second framewise data quality index is called DVARS, which is calculated in each volume as the RMS of the derivatives of the timecourses of all within-brain voxels. DVARS thus measures how much image intensity has changed from one frame to the next. This measure was conceived of as a logical extension of the trends shown in Figures and , where epochs of head movement coincide with epochs of high-amplitude BOLD signal changes. Such plots are shown in for two subjects (see also Figure S5
). Note that the plots of framewise displacement and DVARS are similar but not identical. In particular, framewise displacement measures tend to be temporally focused (sharp peaks) in contrast to the broader peaks of the DVARS measure. Additionally, the signal-to-noise ratio is larger for framewise displacement than for DVARS (Figures S5, S6
). For moderate to large movements, both indices identify very similar portions of the data (big peaks occur at nearly identical timepoints). If one also wishes to identify small movements, framewise displacement may more sensitive due to the lower “floor” in the signal (see Figures S5, S6
). Note that framewise displacement arises from realignment parameters calculated in fMRI preprocessing steps, whereas the DVARS measure reflects image intensity, which (if no realignment parameters are regressed) has no explicit relation to the movement measures other than the alignment process itself. It is presently unclear whether one index captures data quality better than the other, but the ease of producing either measure and the similarity of frame indexing that each measure produces render the issue moot in operational terms when only large movements are sought. After studying the plots of dozens of healthy adults, values of 0.5 for framewise displacement and 0.5% ΔBOLD for DVARS were chosen to represent values well above the norm found in still subjects (see Figure S5
for examples of still subjects).
Two framewise indices of data quality, and a method for flagging frames of suspect quality
A temporal mask was generated from each index, marking frames whose framewise displacement or DVARS exceeded the cutoffs set above. show the temporal masks generated from each index in two subjects, and the cutoffs themselves are shown as dotted lines in the plots above. These temporal masks were augmented by also marking the frames 1 back and 2 forward from any marked frames to accommodate temporal smoothing of BOLD data in functional connectivity processing and re-establishment of steady-state spins. Since reasonable arguments underlie each measure as an index of data quality, we conservatively chose to use an intersection of the two temporal masks to generate a final temporal mask. All removed frames must thus 1) be high-motion frames, and 2) display evidence of widespread and/or large amplitude changes in BOLD signal. When any operations were performed upon a subject’s data, the temporal mask was applied to eliminate marked frames from the analysis. Importantly, the current analysis is designed to identify only the most egregiously suspect frames of data in order to explore how a relatively small number of “bad” frames impact the data, rather than to completely excise movement-related artifact.
Even with this conservative approach to identifying periods of motion in a relatively still cohort of children, the temporal masks indicated that approximately 25% of the data from Cohort 1 was severely contaminated with motion artifact (). The subject inclusion criteria for this study were identical to the traditional criteria employed in our laboratory, with the added requirement that at least 125 frames (~5 min) of data must remain after scrubbing. No limitations were placed on the percentage of data that scrubbing could remove as long as this minimum amount of data remained. These inclusion criteria were employed because our aim was a) to describe what happened if (any amount of) motion-contaminated data was removed from a scan and b) to recover as much data from compromised scans as possible. Figure S7
shows the proportion of data removed from each subject in this study. Importantly, periods of motion could be brief or extended: although many motion epochs last only one or two TRs, many epochs lasting 5, 10, or even dozens of TRs were also identified (see Figure S8
). The varying extents of periods of movement suggest that the induced BOLD signal changes may have varying durations, some of which may be within the low-frequency window that characterizes rs-fcMRI data.
To test the effects of high-motion frames on rs-fcMRI correlations, this scrubbing procedure was applied to four cohorts of healthy subjects to produce four unscrubbed and four scrubbed datasets. Within each cohort (for N subjects), the 264 ROIs described previously were applied to the scrubbed and the unscrubbed data to produce timecourses and seed correlation maps. Pearson correlations between seed timecourses were calculated to produce 264×264×N matrices of scrubbed and unscrubbed data in each subject. The unscrubbed matrices were subtracted from the scrubbed matrices to produce Δr matrices.
The effects of scrubbing high-motion frames from the data are readily visible on inspection. display seed correlation maps from a seed in medial parietal cortex (−7 −55 27) in unscrubbed (top) and scrubbed (bottom) data from two subjects in Cohort 1. Scrubbing removed 35% and 39% of the data from these subjects, respectively. The seed ROI is a member of the default mode network, and the correlation maps in scrubbed data demonstrate more characteristic topography (see the differences in medial prefrontal cortex, for example) than the maps from unscrubbed data. Prior to scrubbing, one is struck by the incompleteness of correlations within the default mode network, whereas after scrubbing, it is clear that the seed is correlated with the canonical regions of the entire default mode network. Such changes in correlation patterns can be found in many subjects. displays changes in correlation values between medial parietal and medial prefrontal cortex seeds for the 22 subjects in Cohort 1 in unscrubbed and scrubbed data. Correlations between these two ROIs, which are both members of the default mode network, are substantially increased in most subjects. A natural reaction is to ask whether such changes are significant and to demand direct comparisons or t-tests before taking these results seriously. As we will demonstrate shortly, the changes in correlations depend (naturally) upon the amount of data that is removed by scrubbing, which is in turn dependent upon framewise displacement and DVARS measures. For a given threshold, greater amounts of movement will produce greater (and more often significant) changes. Likewise, for a given amount of movement, more stringent scrubbing settings will remove more data and produce greater effects.
Examples of how motion scrubbing impacts rs-fcMRI data
More comprehensive investigations of motion scrubbing reveal systematic effects throughout the brain. plots the mean Δr matrix from Cohort 1 against the Euclidean distance between the ROIs that produced the correlations. Motion scrubbing tends to decrease many short-range correlations, and to increase many medium- to long-range correlations. To check that these changes did not arise simply as a result of removing frames, the temporal masks within each subject were randomized to remove an identical amount of data, in identical-sized chunks, but at random. This “random scrubbing” was performed 10 times, always with the result shown in , which shows no systematic effects of distance upon Δr. The difference in the amplitudes of Δr effects is highly significant (paired two-tail t-test, t = 251; p=0). A linear fit of Δr in motion scrubbed data to Euclidean distance has a slope of 4.5 ± 0.01 × 10−4 Δr/mm with an r2 of 0.18, whereas a fit to random scrubbing data has a much shallower slope of 0.74 ± 0.04 × 10−4 Δr/mm and an r2 of 0.03, explaining almost no variance in the data.
Scrubbing high-motion frames from rs-fcMRI data decreases short-distance correlations and augments long-distance correlations
The spatial distribution of these changes is shown in , which plots changes in correlation on a brain. Blue vectors decrease with scrubbing, red vectors increase with scrubbing, and black spheres identify ROI locations. As indexed by absolute value of the change, the top 0.5%, 1%, and 2% of Δr are shown. Short blue vectors pepper the cortex, and long red lines connect distant ROIs. plots Δr in terms of the projection of pairwise correlations onto the X, Y, and Z axes of the brain. Here, again, the dependence of Δr upon distance is clear. Additionally, these plots show that lateral relationships (along the X axis) tend to be decreased by scrubbing, whereas vertical or anterior-posterior relationships tend to be increased by scrubbing. This set of observations is consonant with the effects shown in Figure S4
, in which head motion produced symmetric effects about the X axis, but produced strong BOLD signal changes of opposite sign in the anterior-posterior and dorsal-ventral directions. Changes in pitch (e.g., head nodding) are a predominant form of motion in many scans, and could produce such effects.
The spatial distribution of scrubbing effects upon correlations
Scrubbing produces direction- and distance-dependent changes in correlations
Similar results are found in three additional cohorts (Cohorts 2-4). , and 8G all show the trend for scrubbing to decrease short-distance correlations and to augment medium- to long-distance correlations. It is clear that the effect is strongest in children, intermediate in adolescents, and weakest in adults. The magnitude of the Δr effect is significantly different between cohorts (one-factor ANOVA, main effect of cohort: p = 0; post-hoc two-sample two-tail t-tests demonstrate that 55.3% of child-adult, 8.5% of child-adolescent, and 2.1% of adolescent-adult comparisons of Δr were significant beyond p < 0.05, FDR corrected), and is related to how much data was scrubbed from the dataset, which in turn is related to the amount of movement the cohorts possessed (see ). Although the effects are weaker in adolescents and adults, they are certainly present, as the plots of motion scrubbing and random scrubbing in Figure S9
make clear. The brain surfaces in present the spatial distribution of the top 2% of Δr changes in each cohort. No particular spatial patterning is clear across cohorts, other than the tendency for blue vectors to be shorter than the red vectors.
Similar effects of scrubbing are found in 3 additional cohorts
A question of particular interest to the neuroimaging community is whether these findings generalize beyond particular scanners, institutions, study populations, and acquisition sequences. The datasets reported in this paper represent a single institution, two scanners with two field strengths and two acquisition sequences, and three age ranges (see Methods). Scrubbing methods have also been applied to several datasets other than the ones reported here, and the effects are present in every dataset from every site examined thus far (at present, four sites). This represents data acquired in several scanners (Philips and Siemens) at multiple field strengths (1.5T and 3T) using multiple acquisition sequences. The effects do not appear to be particular to any study population (they are present in clinical adult cohorts, in neonatal cohorts, etc.). As such, this artifact appears to be a general feature of functional connectivity MRI. It is probable that particular aspects of acquisition (e.g. gradient sequence, spatial or temporal resolution, etc) may render data more or less sensitive to motion-related effects, though we are unable to offer any specific observations or recommendations at this point. It is worth noting that framewise displacement estimates should be relatively uniform across sites, scanners, and sequences, but that the DVARs measure may vary across these parameters, since it indexes changes in signal intensity.
A related question is whether this artifact is produced and/or countered by particular aspects of data processing. For any analysis it is standard practice to realign fMRI data across scans. After fMRI preprocessing, a variety of functional connectivity processing strategies may be used to form rs-fcMRI data. These approaches typically include spatial blurring, temporal bandpassing, and some version of “artifact removal”, whether by regression of nuisance variables or component removal or other methods. The data presented in this paper follows a functional connectivity processing stream that uses a multiple regression of nuisance variables as a method to reduce noise and artifact in functional connectivity data (Fox et al., 2009
). Typical regressors include signals from white matter, ventricles, and the whole brain, the derivatives of those 3 signals, the 6 head realignment estimates, and the derivatives of each of those estimates (18 regressors total). An important concern is that motion-related artifacts might actually have been introduced to the data in the regression process. plots Δr against Euclidean distance for Cohort 1 beginning with the standard functional connectivity processing stream, then progressively removing elements of the regression, and finally removing the regression altogether (so that the data have only been realigned, registered, blurred, and bandpassed). In each case the artifact is present, excluding these regressions as a source of this effect. This indicates that the motion-related dependence of correlation strength upon distance is either inherent in the data (presumably, due to motion), or that it is produced by the widely used processes of data realignment, blurring, or bandpassing. In terms of countering the motion-induced correlations, the regressions in this processing stream have a partial but incomplete effect: the spread of the histogram of Δr values is clearly reduced by the regressions, but the artifact persists through all aspects of functional connectivity processing. It is possible that other approaches to functional connectivity processing (e.g., ICA) may fare better in removing this motion-related artifact, and we encourage users of other approaches to test their data for similar effects.
Motion-induced colored noise does not arise from standard regressions in functional connectivity processing
We now demonstrate how scrubbing can alter fundamental conclusions about patterns of functional connectivity. Across typical development, several groups, including our own, have reported a reorganization of functional connectivity, such that short-distance correlations tend to decrease with age, whereas long-distance relationships between functionally related brain regions tend to increase with age (for a review of the developmental literature, see (Power et al., 2010
)). This pattern is, unfortunately, also what one would predict from a motion-related artifact (). presents the community assignments of child and adult datasets (Cohorts 1 and 3, see ) before and after scrubbing. Here, colors in each panel indicate sub-networks within the brain-wide network of 264 ROIs. Scrubbing produced little change in the community structure of adult functional networks, but it produced substantial changes in the child functional networks. What began as largely local, non-distributed communities in children (e.g. the orange community in children) became distributed modules with closer resemblance to adult modules (e.g. the yellow or red modules) upon scrubbing. This reflects a fundamental reorganization of the child network into a more adult-like distributed architecture that includes intact default and fronto-parietal sub-networks. These changes in network architecture can be quantified by normalized mutual information, which indicates that community assignments between children and adults before scrubbing (NMI = 0.56) become more similar after scrubbing (NMI = 0.70). This increase is not seen upon random scrubbing (over 10 repetitions, NMI = 0.58 ± 0.01). Another way to quantify this set of observations is to note that scrubbing reduces the number of significant differences in pairwise correlations between children and adults by over 30% (from 608 to 401, p < 0.05 FDR corrected, two-tail two-sample t-test). These findings suggest that at least some of the developmental differences previously reported can be accounted for by motion-related artifact.
These analyses employed the standard scrubbing regime used throughout this manuscript, and are intended as proof-of-principle that even a modest amount of data removal can alter patterns of functional connectivity. A more definitive and comprehensive investigation of developmental functional connectivity is in preparation, utilizing more stringent scrubbing criteria (see Figure S10
for an example of how scrubbing affects statistical power). Additionally, we are exploring the incorporation of temporal masks in the multiple regression stage, since large-amplitude motion-related changes are likely to decrease the beta weights of regressors, which could differentially impact subject data across development.