A comparison of denoising pipelines in high temporal resolution task-based functional magnetic resonance imaging data

Multifaceted neural and vascular pathologies after pediatric mild traumatic brain injury

Dynamic changes in neurodevelopment and cognitive functioning occur during adolescence, including a switch from reactive to more proactive forms of cognitive control, including response inhibition. Pediatric mild traumatic brain injury (pmTBI) affects these cognitions immediately post-injury, but the role of vascular versus neural injury in cognitive dysfunction remains debated. This study consecutively recruited 214 sub-acute pmTBI (8-18 years) and age/sex-matched healthy controls (HC; N = 186), with high retention rates (>80%) at four months post-injury. Multimodal imaging (functional MRI during response inhibition, cerebral blood flow and cerebrovascular reactivity) assessed for pathologies within the neurovascular unit. Patients exhibited increased errors of commission and hypoactivation of motor circuitry during processing of probes. Evidence of increased/delayed cerebrovascular reactivity within motor circuitry during hypercapnia was present along with normal perfusion. Neither age-at-injury nor post-concussive symptom load were strongly associated with imaging abnormalities. Collectively, mild cognitive impairments and clinical symptoms may continue up to four months post-injury. Prolonged dysfunction within the neurovascular unit was observed during proactive response inhibition, with preliminary evidence that neural and pure vascular trauma are statistically independent. These findings suggest pmTBI is characterized by multifaceted pathologies during the sub-acute injury stage that persist several months post-injury.

Denoising task-related fMRI: Balancing noise reduction against signal loss

Preprocessing fMRI data requires striking a fine balance between conserving signals of interest and removing noise. Typical steps of preprocessing include motion correction, slice timing correction, spatial smoothing, and high-pass filtering. However, these standard steps do not remove many sources of noise. Thus, noise-reduction techniques, for example, CompCor, FIX, and ICA-AROMA have been developed to further improve the ability to draw meaningful conclusions from the data. The ability of these techniques to minimize noise while conserving signals of interest has been tested almost exclusively in resting-state fMRI and, only rarely, in task-related fMRI. Application of noise-reduction techniques to task-related fMRI is particularly important given that such procedures have been shown to reduce false positive rates. Little remains known about the impact of these techniques on the retention of signal in tasks that may be associated with systemic physiological changes. In this paper, we compared two ICA-based, that is FIX and ICA-AROMA, two CompCor-based noise-reduction techniques, that is aCompCor, and tCompCor, and standard preprocessing using a large (n = 101) fMRI dataset including noxious heat and non-noxious auditory stimulation. Results show that preprocessing using FIX performs optimally for data obtained using noxious heat, conserving more signals than CompCor-based techniques and ICA-AROMA, while removing only slightly less noise. Similarly, for data obtained during non-noxious auditory stimulation, FIX noise-reduction technique before analysis with a covariate of interest outperforms the other techniques. These results indicate that FIX might be the most appropriate technique to achieve the balance between conserving signals of interest and removing noise during task-related fMRI.

Static and dynamic functional connectome reveals reconfiguration profiles of whole-brain network across cognitive states

Assessment of functional connectivity (FC) has revealed a great deal of knowledge about the macroscale spatiotemporal organization of the brain network. Recent studies found task-versus-rest network reconfigurations were crucial for cognitive functioning. However, brain network reconfiguration remains unclear among different cognitive states, considering both aggregate and time-resolved FC profiles. The current study utilized static FC (sFC, i.e., long timescale aggregate FC) and sliding window-based dynamic FC (dFC, i.e., short timescale time-varying FC) approaches to investigate the similarity and alterations of edge weights and network topology at different cognitive loads, particularly their relationships with specific cognitive process. Both dFC/sFC networks showed subtle but significant reconfigurations that correlated with task performance. At higher cognitive load, brain network reconfiguration displayed increased functional integration in the sFC-based aggregate network, but faster and larger variability of modular reorganization in the dFC-based time-varying network, suggesting difficult tasks require more integrated and flexible network reconfigurations. Moreover, sFC-based network reconfigurations mainly linked with the sensorimotor and low-order cognitive processes, but dFC-based network reconfigurations mainly linked with the high-order cognitive process. Our findings suggest that reconfiguration profiles of sFC/dFC networks provide specific information about cognitive functioning, which could potentially be used to study brain function and disorders.

The optimized combination of aCompCor and ICA-AROMA to reduce motion and physiologic noise in task fMRI data

One of the main challenges in fMRI processing is filtering the task BOLD signals from the noise. Independent component analysis with automatic removal of motion artifacts (ICA-AROMA) reduces motion artifacts by identifying ICA noise components based on their location at the brain edges and cerebrospinal fluid (CSF), high frequency content and correlation with motion regressors. In anatomical component correction (aCompCor), physiological noise regressors extracted from CSF were regressed out from the fMRI time series. In this study, we compared three methods to combine aCompCor and ICA-AROMA denoising in one denoising step. In the first analysis, we regressed the temporal signals of the ICA components identified as noise by ICA-AROMA together with the noise signals determined by aCompCor from the fMRI signals. For the second and third analyses, the correlation between the temporal signals of the ICA components and the aCompCor noise signals was used as an additional criterion to identify the noise components. In the second analysis, the temporal signals of the ICA components classified as noise were regressed from the fMRI signals. In the third analysis, the noise components were removed. To compare the denoising strategies, we examined the fractional amplitude of low-frequency fluctuations (fALFF) and the overlap between the contrast maps. Our results revealed that including the aCompCor noise signals as regressors in ICA-AROMA resulted in more correctly identified noise components, higher fALFF values, and larger activation maps. Moreover, combining the temporal signals of the noise components identified by ICA-AROMA with the aCompCor signals in a noise regression matrix resulted in deactivations. These results suggest that using the correlation between the ICA component temporal signals and the aCompCor signals as noise identification criteria in ICA-AROMA is the best approach for combining both denoising methods.

A methodological checklist for fMRI drug cue reactivity studies: development and expert consensus

Cue reactivity is one of the most frequently used paradigms in functional magnetic resonance imaging (fMRI) studies of substance use disorders (SUDs). Although there have been promising results elucidating the neurocognitive mechanisms of SUDs and SUD treatments, the interpretability and reproducibility of these studies is limited by incomplete reporting of participants' characteristics, task design, craving assessment, scanning preparation and analysis decisions in fMRI drug cue reactivity (FDCR) experiments. This hampers clinical translation, not least because systematic review and meta-analysis of published work are difficult. This consensus paper and Delphi study aims to outline the important methodological aspects of FDCR research, present structured recommendations for more comprehensive methods reporting and review the FDCR literature to assess the reporting of items that are deemed important. Forty-five FDCR scientists from around the world participated in this study. First, an initial checklist of items deemed important in FDCR studies was developed by several members of the Enhanced NeuroImaging Genetics through Meta-Analyses (ENIGMA) Addiction working group on the basis of a systematic review. Using a modified Delphi consensus method, all experts were asked to comment on, revise or add items to the initial checklist, and then to rate the importance of each item in subsequent rounds. The reporting status of the items in the final checklist was investigated in 108 recently published FDCR studies identified through a systematic review. By the final round, 38 items reached the consensus threshold and were classified under seven major categories: 'Participants' Characteristics', 'General fMRI Information', 'General Task Information', 'Cue Information', 'Craving Assessment Inside Scanner', 'Craving Assessment Outside Scanner' and 'Pre- and Post-Scanning Considerations'. The review of the 108 FDCR papers revealed significant gaps in the reporting of the items considered important by the experts. For instance, whereas items in the 'General fMRI Information' category were reported in 90.5% of the reviewed papers, items in the 'Pre- and Post-Scanning Considerations' category were reported by only 44.7% of reviewed FDCR studies. Considering the notable and sometimes unexpected gaps in the reporting of items deemed to be important by experts in any FDCR study, the protocols could benefit from the adoption of reporting standards. This checklist, a living document to be updated as the field and its methods advance, can help improve experimental design, reporting and the widespread understanding of the FDCR protocols. This checklist can also provide a sample for developing consensus statements for protocols in other areas of task-based fMRI.

A sub+cortical fMRI-based surface parcellation

Both cortical and subcortical structures are organized into a large number of distinct areas reflecting functional and cytoarchitectonic differences. Mapping these areas is of fundamental importance to neuroscience. A central obstacle to this task is the inaccuracy associated with bringing results from individuals into a common space. The vast individual differences in morphology pose a serious problem for volumetric registration. Surface‐based approaches fare substantially better, but have thus far been used only for cortical parcellation, leaving subcortical parcellation in volumetric space. We extend the surface‐based approach to include also the subcortical deep gray‐matter structures, thus achieving a uniform representation across both cortex and subcortex, suitable for use with surface‐based metrics that span these structures, for example, white/gray contrast. Using data from the Enhanced Nathan Klein Institute—Rockland Sample, limited to individuals between 19 and 69 years of age, we generate a functional parcellation of both the cortical and subcortical surfaces. To assess this extended parcellation, we show that (a) our parcellation provides greater homogeneity of functional connectivity patterns than do arbitrary parcellations matching in the number and size of parcels; (b) our parcels align with known cortical and subcortical architecture; and (c) our extended functional parcellation provides an improved fit to the complexity of life‐span (6–85 years) changes in white/gray contrast data compared to arbitrary parcellations matching in the number and size of parcels, supporting its use with surface‐based measures. We provide our extended functional parcellation for the use of the neuroimaging community.

Persistent alterations in cerebrovascular reactivity in response to hypercapnia following pediatric mild traumatic brain injury

Much attention has been paid to the effects of mild traumatic brain injury (mTBI) on cerebrovascular reactivity in adult populations, yet it remains understudied in pediatric injury. In this study, 30 adolescents (12-18 years old) with pediatric mTBI (pmTBI) and 35 age- and sex-matched healthy controls (HC) underwent clinical and neuroimaging assessments during sub-acute (6.9 ± 2.2 days) and early chronic (120.4 ± 11.7 days) phases of injury. Relative to controls, pmTBI reported greater initial post-concussion symptoms, headache, pain, and anxiety, resolving by four months post-injury. Patients reported increased sleep issues and exhibited deficits in processing speed and attention across both visits. In grey-white matter interface areas throughout the brain, pmTBI displayed increased maximal fit/amplitude of a time-shifted end-tidal CO₂ regressor to blood oxygen-level dependent response relative to HC, as well as increased latency to maximal fit. The alterations persisted through the early chronic phase of injury, with maximal fit being associated with complaints of ongoing sleep disturbances during post hoc analyses but not cognitive measures of processing speed or attention. Collectively, these findings suggest that deficits in the speed and degree of cerebrovascular reactivity may persist longer than current conceptualizations about clinical recovery within 30 days.

Noise removal in resting-state and task fMRI: functional connectivity and activation maps

OBJECTIVE

Blood-oxygenated-level dependent (BOLD)-based functional magnetic resonance imaging (fMRI) is a widely used non-invasive tool for mapping brain function and connectivity. However, the BOLD signal is highly affected by non-neuronal contributions arising from head motion, physiological noise and scanner artefacts. Therefore, it is necessary to recover the signal of interest from the other noise-related fluctuations to obtain reliable functional connectivity (FC) results. Several pre-processing pipelines have been developed, mainly based on nuisance regression and independent component analysis (ICA). The aim of this work was to investigate the impact of seven widely used denoising methods on both resting-state and task fMRI.

APPROACH

Task fMRI can provide some ground truth given that the task administered has well established brain activations. The resulting cleaned data were compared using a wide range of measures: motion evaluation and data quality, resting-state networks and task activations, FC.

MAIN RESULTS

Improved signal quality and reduced motion artefacts were obtained with all advanced pipelines, compared to the minimally pre-processed data. Larger variability was observed in the case of brain activation and FC estimates, with ICA-based pipelines generally achieving more reliable and accurate results.

SIGNIFICANCE

This work provides an evidence-based reference for investigators to choose the most appropriate method for their study and data.

Proactive inhibition deficits with normal perfusion after pediatric mild traumatic brain injury

Although much attention has been generated in popular media regarding the deleterious effects of pediatric mild traumatic brain injury (pmTBI), a paucity of empirical evidence exists regarding the natural course of biological recovery. Fifty pmTBI patients (12–18 years old) were consecutively recruited from Emergency Departments and seen approximately 1 week and 4 months post‐injury in this prospective cohort study. Data from 53 sex‐ and age‐matched healthy controls (HC) were also collected. Functional magnetic resonance imaging was obtained during proactive response inhibition and at rest, in conjunction with independent measures of resting cerebral blood flow. High temporal resolution imaging enabled separate modeling of neural responses for preparation and execution of proactive response inhibition. A priori predictions of failed inhibitory responses (i.e., hyperactivation) were observed in motor circuitry (pmTBI>HC) and sensory areas sub‐acutely and at 4 months post‐injury. Paradoxically, pmTBI demonstrated hypoactivation (HC>pmTBI) during target processing, along with decreased activation within prefrontal cognitive control areas. Functional connectivity within motor circuitry at rest suggested that deficits were limited to engagement during the inhibitory task, whereas normal resting cerebral perfusion ruled out deficits in basal perfusion. In conclusion, current results suggest blood oxygen‐level dependent deficits during inhibitory control may exceed commonly held beliefs about physiological recovery following pmTBI, potentially lasting up to 4 months post‐injury.

A comparison of denoising pipelines in high temporal resolution task-based functional magnetic resonance imaging data

It has been known for decades that head motion/other artifacts affect the blood oxygen level-dependent signal. Recent recommendations predominantly focus on denoising resting state data, which may not apply to task data due to the different statistical relationships that exist between signal and noise sources. Several blind-source denoising strategies (FIX and AROMA) and more standard motion parameter (MP) regression (0, 12, or 24 parameters) analyses were therefore compared across four sets of event-related functional magnetic resonance imaging (erfMRI) and block-design (bdfMRI) datasets collected with multiband 32- (repetition time [TR] = 460 ms) or older 12-channel (TR = 2,000 ms) head coils. The amount of motion varied across coil designs and task types. Quality control plots indicated small to moderate relationships between head motion estimates and percent signal change in both signal and noise regions. Blind-source denoising strategies eliminated signal as well as noise relative to MP24 regression; however, the undesired effects on signal depended both on algorithm (FIX > AROMA) and design (bdfMRI > erfMRI). Moreover, in contrast to previous results, there were minimal differences between MP12/24 and MP0 pipelines in both erfMRI and bdfMRI designs. MP12/24 pipelines were detrimental for a task with both longer block length (30 ± 5 s) and higher correlations between head MPs and design matrix. In summary, current results suggest that there does not appear to be a single denoising approach that is appropriate for all fMRI designs. However, even nonaggressive blind-source denoising approaches appear to remove signal as well as noise from task-related data at individual subject and group levels.