Typicality of functional connectivity robustly captures motion artifacts in rs-fMRI across datasets, atlases, and preprocessing pipelines

Implementing ABCD studyⓇ MRI sequences for multi-site cohort studies: Practical guide to necessary steps, preprocessing methods, and challenges

Large multi-site studies that combine magnetic resonance imaging (MRI) data across research sites present exceptional opportunities to advance neuroscience research. However, scanner or site variability and non-standardised image acquisition protocols, data processing and analysis pipelines can adversely affect the reliability and repeatability of MRI derived brain measures. We implemented a standardised MRI protocol based on that used in the Adolescent Brain Cognition Development (ABCD)Ⓡ study in two sites, and across four MRI scanners. Twice repeated measurements of a single healthy volunteer were obtained in two sites and in four 3T MRI scanners (vendors: Siemens, Philips, and GE). Imaging data included anatomical scans (T1 weighted, T2 weighted), diffusion weighted imaging (DWI) and resting state functional MRI (rs-fMRI). Standardised containerized pipelines were utilised to pre-process the data and different image quality metrics and test-retest variability of different brain metrics were evaluated. The implementation of the MRI protocols was possible with minor adjustments in acquisition (e.g. repetition time (TR), higher b-values) and exporting (DICOM formats) of images due to different technical performance of the scanners. This study provides practical insights into the implementation of standardised sequences and data processing for multisite studies, showcase the benefits of containerised preprocessing tools, and highlights the need for careful optimisation of multisite image acquisition.

Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression

Brain activity during the resting state is widely used to examine brain organization, cognition and alterations in disease states. While it is known that neuromodulation and the state of alertness impact resting-state activity, neural mechanisms behind such modulation of resting-state activity are unknown. In this work, we used a computational model to demonstrate that change in excitability and recurrent connections, due to cholinergic modulation, impacts resting-state activity. The results of such modulation in the model match closely with experimental work on direct cholinergic modulation of Default Mode Network (DMN) in rodents. We further extended our study to the human connectome derived from diffusion-weighted MRI. In human resting-state simulations, an increase in cholinergic input resulted in a brain-wide reduction of functional connectivity. Furthermore, selective cholinergic modulation of DMN closely captured experimentally observed transitions between the baseline resting state and states with suppressed DMN fluctuations associated with attention to external tasks. Our study thus provides insight into potential neural mechanisms for the effects of cholinergic neuromodulation on resting-state activity and its dynamics.

Resting-state functional MRI in multicenter studies on multiple sclerosis: a report on raw data quality and functional connectivity features from the Italian Neuroimaging Network Initiative

The Italian Neuroimaging Network Initiative (INNI) is an expanding repository of brain MRI data from multiple sclerosis (MS) patients recruited at four Italian MRI research sites. We describe the raw data quality of resting-state functional MRI (RS-fMRI) time-series in INNI and the inter-site variability in functional connectivity (FC) features after unified automated data preprocessing. MRI datasets from 489 MS patients and 246 healthy control (HC) subjects were retrieved from the INNI database. Raw data quality metrics included temporal signal-to-noise ratio (tSNR), spatial smoothness (FWHM), framewise displacement (FD), and differential variation in signals (DVARS). Automated preprocessing integrated white-matter lesion segmentation (SAMSEG) into a standard fMRI pipeline (fMRIPrep). FC features were calculated on pre-processed data and harmonized between sites (Combat) prior to assessing general MS-related alterations. Across centers (both groups), median tSNR and FWHM ranged from 47 to 84 and from 2.0 to 2.5, and median FD and DVARS ranged from 0.08 to 0.24 and from 1.06 to 1.22. After preprocessing, only global FC-related features were significantly correlated with FD or DVARS. Across large-scale networks, age/sex/FD-adjusted and harmonized FC features exhibited both inter-site and site-specific inter-group effects. Significant general reductions were obtained for somatomotor and limbic networks in MS patients (vs. HC). The implemented procedures provide technical information on raw data quality and outcome of fully automated preprocessing that might serve as reference in future RS-fMRI studies within INNI. The unified pipeline introduced little bias across sites and appears suitable for multisite FC analyses on harmonized network estimates.

Rich-club reorganization of functional brain networks in acute mild traumatic brain injury with cognitive impairment

BACKGROUND

Mild traumatic brain injury (mTBI) is typically characterized by temporally limited cognitive impairment and regarded as a brain connectome disorder. Recent findings have suggested that a higher level of organization named the "rich-club" may play a central role in enabling the integration of information and efficient communication across different systems of the brain. However, the alterations in rich-club organization and hub topology in mTBI and its relationship with cognitive impairment after mTBI have been scarcely elucidated.

METHODS

Resting-state functional magnetic resonance imaging (rs-fMRI) data were collected from 88 patients with mTBI and 85 matched healthy controls (HCs). Large-scale functional brain networks were established for each participant. Rich-club organizations and network properties were assessed and analyzed between groups. Finally, we analyzed the correlations between the cognitive performance and changes in rich-club organization and network properties.

RESULTS

Both mTBI and HCs groups showed significant rich-club organization. Meanwhile, the rich-club organization was aberrant, with enhanced functional connectivity (FC) among rich-club nodes and peripheral regions in acute mTBI. In addition, significant differences in partial global and local network topological property measures were found between mTBI patients and HCs (P<0.01). In patients with mTBI, changes in rich-club organization and network properties were found to be related to early cognitive impairment after mTBI (P<0.05).

CONCLUSIONS

Our findings suggest that such patterns of disruption and reorganization will provide the basic functional architecture for cognitive function, which may subsequently be used as an earlier biomarker for cognitive impairment after mTBI.

Brain Functional Connectivity Asymmetry: Left Hemisphere Is More Modular

Graph-theoretical approaches are increasingly used to study the brain and may enhance our understanding of its asymmetries. In this paper, we hypothesize that the structure of the left hemisphere is, on average, more modular. To this end, we analyzed resting-state functional magnetic resonance imaging data of 90 healthy subjects. We computed functional connectivity by Pearson’s correlation coefficient, turned the matrix into an unweighted graph by keeping a certain percentage of the strongest connections, and quantified modularity separately for the subgraph formed by each hemisphere. Our results show that the left hemisphere is more modular. The result is consistent across a range of binarization thresholds, regardless of whether the two hemispheres are thresholded together or separately. This illustrates that graph-theoretical analysis can provide a robust characterization of lateralization of brain functional connectivity.

Blood Oxygen Level-Dependent Lag Patterns Differ Between Rest and Task Conditions, but Are Largely Typical in Autism

Background/Introduction: Autism spectrum disorder (ASD) is characterized by atypical functional connectivity (FC) within and between distributed brain networks. However, FC findings have often been inconsistent, possibly due to a focus on static FC rather than brain dynamics. Lagged connectivity analyses aim at evaluating temporal latency, and presumably neural propagation, between regions. This approach may, therefore, reveal a more detailed picture of network organization in ASD than traditional FC methods. Methods: The current study evaluated whole-brain lag patterns in adolescents with ASD (n = 28) and their typically developing peers (n = 22). Functional magnetic resonance imaging data were collected during rest and during a lexico-semantic decision task. Optimal lag was calculated for each pair of regions of interest by using cross-covariance, and mean latency projections were calculated for each region. Results: Latency projections did not regionally differ between groups, with the same regions emerging among the "earliest" and "latest." Although many of the longest absolute latencies were preserved across resting-state and task conditions, lag patterns overall were affected by condition, as many regions shifted toward zero-lag during task performance. Lag structure was also strongly associated with literature-derived estimates of arterial transit time. Discussion: Results suggest that lag patterns are broadly typical in ASD but undergo changes during task performance. Moreover, lag patterns appear to reflect a combination of neural and vascular sources, which should be carefully considered when interpreting lagged FC.

Promises and pitfalls of topological data analysis for brain connectivity analysis

Developing sensitive and reliable methods to distinguish normal and abnormal brain states is a key neuroscientific challenge. Topological Data Analysis, despite its relative novelty, already generated many promising applications, including in neuroscience. We conjecture its prominent tool of persistent homology may benefit from going beyond analysing structural and functional connectivity to effective connectivity graphs capturing the direct causal interactions or information flows. Therefore, we assess the potential of persistent homology to directed brain network analysis by testing its discriminatory power in two distinctive examples of disease-related brain connectivity alterations: epilepsy and schizophrenia. We estimate connectivity from functional magnetic resonance imaging and electrophysiology data, employ Persistent Homology and quantify its ability to distinguish healthy from diseased brain states by applying a support vector machine to features quantifying persistent homology structure. We show how this novel approach compares to classification using standard undirected approaches and original connectivity matrices. In the schizophrenia classification, topological data analysis generally performs close to random, while classifications from raw connectivity perform substantially better; potentially due to topographical, rather than topological, specificity of the differences. In the easier task of seizure discrimination from scalp electroencephalography data, classification based on persistent homology features generally reached comparable performance to using raw connectivity, albeit with typically smaller accuracies obtained for the directed (effective) connectivity compared to the undirected (functional) connectivity. Specific applications for topological data analysis may open when direct comparison of connectivity matrices is unsuitable - such as for intracranial electrophysiology with individual number and location of measurements. While standard homology performed overall better than directed homology, this could be due to notorious technical problems of accurate effective connectivity estimation.

Predictive utility of task-related functional connectivity vs. voxel activation

Functional connectivity, both in resting state and task performance, has steadily increased its share of neuroimaging research effort in the last 1.5 decades. In the current study, we investigated the predictive utility regarding behavioral performance and task information for 240 participants, aged 20–77, for both voxel activation and functional connectivity in 12 cognitive tasks, belonging to 4 cognitive reference domains (Episodic Memory, Fluid Reasoning, Perceptual Speed, and Vocabulary). We also added a model only comprising brain-structure information not specifically acquired during performance of a cognitive task. We used a simple brain-behavioral prediction technique based on Principal Component Analysis (PCA) and regression and studied the utility of both modalities in quasi out-of-sample predictions, using split-sample simulations (= 5-fold Monte Carlo cross validation) with 1,000 iterations for which a regression model predicting a cognitive outcome was estimated in a training sample, with a subsequent assessment of prediction success in a non-overlapping test sample. The sample assignments were identical for functional connectivity, voxel activation, and brain structure, enabling apples-to-apples comparisons of predictive utility. All 3 models that were investigated included the demographic covariates age, gender, and years of education. A minimal reference model using simple linear regression with just these 3 covariates was included for comparison as well and was evaluated with the same resampling scheme as described above. Results of the comparison between voxel activation and functional connectivity were mixed and showed some dependency on cognitive outcome; however, mean differences in predictive utility between voxel activation and functional connectivity were rather small in terms of within-modality variability or predictive success. More notably, only in the case of Fluid Reasoning did concurrent functional neuroimaging provided compelling about cognitive performance beyond structural brain imaging or the minimal reference model.

Typicality of functional connectivity robustly captures motion artifacts in rs-fMRI across datasets, atlases, and preprocessing pipelines

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.