Biology subjects

Eickhoff, S. B.

Publications and source records attributed to Eickhoff, S. B..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps

Neuroimaging research faces a crisis of reproducibility. With massive sample sizes and greater data complexity, this problem becomes more acute. Software that operates on imaging data defined using the Brain Imaging Data Structure (BIDS) - BIDS Apps - have provided a substantial advance. However, even using BIDS Apps, a full audit trail of data processing is a necessary prerequisite for fully reproducible research. Obtaining a faithful record of the audit trail is challenging - especially for large datasets. Recently, the FAIRly big framework was introduced as a way to facilitate reproducible processing of large-scale data by leveraging DataLad - a version control system for data management. However, the current implementation of this framework was more of a proof of concept, and could not be immediately reused by other investigators for different use cases. Here we introduce the BIDS App Bootstrap (BABS), a user-friendly and generalizable Python package for reproducible image processing at scale. BABS facilitates the reproducible application of BIDS Apps to large-scale datasets. Leveraging DataLad and the FAIRly big framework, BABS tracks the full audit trail of data processing in a scalable way by automatically preparing all scripts necessary for data processing and version tracking on high performance computing (HPC) systems. Currently, BABS supports jobs submissions and audits on Sun Grid Engine (SGE) and Slurm HPCs with a parsimonious set of programs. To demonstrate its scalability, we applied BABS to data from the Healthy Brain Network (HBN; n=2,565). Taken together, BABS allows reproducible and scalable image processing and is broadly extensible via an open-source development model.

neuroscience↗

bioRxiv2023

Charting the brain networks of impulsivity: Meta-analytic synthesis, functional connectivity modelling and neurotransmitter associations

Impulsivity is a multidimensional construct that plays a crucial role in human behaviour and is believed to be a transdiagnostic marker of several psychiatric disorders. However, given its multifaceted nature, comprehensive investigations of its neural correlates are challenging. In this study, we used a multi-modal approach to investigate the functional network organisation of two domains in which impulsivity manifests: decision-making and action control. Within domain ALE meta-analyses identified two distinct functional systems: one located in the default-mode network, associated with value-based judgments and goal-directed decision-making, and the other distributed across higher-order networks associated with cognitive control. These systems were organised into four specialised communities of default-mode, cingulo-insular, frontoparietal, and temporal regions. Integration within those communities was associated with serotonin receptor density. These findings reinforce insights from previous behavioural research and provide substantial evidence for the multidimensional nature of impulsivity on the neural level.

neuroscience↗

bioRxiv2023

Predicting Executive Functioning from Brain Networks: Modality Specificity and Age Effects

Healthy aging is associated with structural and functional network changes in the brain, which have been linked to deterioration in executive functioning (EF), while their neural implementation at the individual level remains unclear. As the biomarker potential of individual resting-state functional connectivity (RSFC) patterns has been questioned, we investigated to what degree individual EF abilities can be predicted from gray-matter volume (GMV), regional homogeneity, fractional amplitude of low-frequency fluctuations (fALFF), and RSFC within EF-related, perceptuo-motor, and whole-brain networks in young and old adults. We examined whether differences in out-of-sample prediction accuracy were modality-specific and depended on age or task-demand levels. Both uni- and multivariate analysis frameworks revealed overall low prediction accuracies and moderate to weak brain-behavior associations (R2 < .07, r < .28), further challenging the idea of finding meaningful markers for individual EF performance with the metrics used. Regional GMV, well linked to overall atrophy, carried the strongest information about individual EF differences in older adults, whereas fALFF, measuring functional variability, did so for younger adults. Our study calls for future research analyzing more global properties of the brain, different task-states and applying adaptive behavioral testing to result in sensitive predictors for young and older adults, respectively.

neuroscience↗

bioRxiv2023

Network and State Specificity in Connectivity-Based Predictions of Individual Behavior

Predicting individual behavior from brain functional connectivity (FC) patterns can contribute to our understanding of human brain functioning. This may apply in particular if predictions are based on features derived from circumscribed, a priori defined functional networks, which improves interpretability. Furthermore, some evidence suggests that task-based FC data may yield more successful predictions of behavior than resting-state FC data. Here, we comprehensively examined to what extent the correspondence of functional network priors and task states with behavioral target domains influences the predictability of individual performance in cognitive, social, and affective tasks. To this end, we used data from the Human Connectome Project for large-scale out-of-sample predictions of individual abilities in working memory (WM), theory-of-mind cognition (SOCIAL), and emotion processing (EMO) from FC of corresponding and non-corresponding states (WM/SOCIAL/EMO/resting-state) and networks (WM/SOCIAL/EMO/whole-brain connectome). Using root mean squared error and coefficient of determination to evaluate model fit revealed that predictive performance was rather poor overall. Predictions from whole-brain FC were slightly better than those from FC in task-specific networks, and a slight benefit of predictions based on FC from task versus resting state was observed for performance in the WM domain. Beyond that, we did not find any significant effects of a correspondence of network, task state, and performance domains. Together, these results suggest that multivariate FC patterns during both task and resting states contain rather little information on individual performance levels, calling for a reconsideration of how the brain mediates individual differences in mental abilities. HighlightsO_LIBetter prediction of behavior from task vs. resting-state FC only in a cognitive domain C_LIO_LILittle evidence for specificity of state, network, or task similarity C_LIO_LIPredicting complex behavior based on FC remains a significant challenge C_LIO_LIWe extend research on brain-based behavior prediction beyond the cognitive domain C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/540387v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@74f08borg.highwire.dtl.DTLVardef@15c7375org.highwire.dtl.DTLVardef@a029e6org.highwire.dtl.DTLVardef@11ed815_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Success versus failure in cognitive control: meta-analytic evidence from neuroimaging studies on error processing

Brain mechanisms of error processing have often been investigated using response interference tasks and focusing on the posterior medial frontal cortex, which is also implicated in resolving response conflict in general. Thereby, the role other brain regions may play has remained undervalued. Here, activation likelihood estimation meta-analyses were used to synthesize the neuroimaging literature on brain activity related to committing errors versus responding successfully in interference tasks and to test for commonalities and differences. The salience network and the temporoparietal junction were commonly recruited irrespective of whether responses were correct or incorrect, pointing towards a general involvement in coping with situations that call for increased cognitive control. The dorsal posterior cingulate cortex, posterior thalamus, and left superior frontal gyrus showed error-specific convergence, which underscores their consistent involvement when performance goals are not met. In contrast, successful responding revealed stronger convergence in the dorsal attention network and lateral prefrontal regions. Underrecruiting these regions in error trials may reflect failures in activating the task-appropriate stimulus-response contingencies necessary for successful response execution.

neuroscience↗

bioRxiv2023

Human cortex development is shaped by molecular and cellular brain systems

Human brain morphology undergoes complex changes over the lifespan. Despite recent progress in tracking brain development via normative models, current knowledge of underlying biological mechanisms is highly limited. We demonstrate that human cortical thickness development and aging trajectories unfold along patterns of molecular and cellular brain organization, traceable from population-level to individual developmental trajectories. During childhood and adolescence, cortex-wide spatial distributions of dopaminergic receptors, inhibitory neurons, glial cell populations, and brain-metabolic features explain up to 50% of variance associated with a lifespan model of regional cortical thickness trajectories. In contrast, modeled cortical thickness change patterns during adulthood are best explained by cholinergic and glutamatergic neurotransmitter receptor and transporter distributions. These relationships are supported by developmental gene expression trajectories and translate to individual longitudinal data from over 8,000 adolescents, explaining up to 59% of developmental change at cohort- and 18% at single-subject level. Integrating neurobiological brain atlases with normative modeling and population neuroimaging provides a biologically meaningful path to understand brain development and aging in living humans.

neuroscience↗

bioRxiv2023

The spatial arrangement of laminar thickness profiles in the human cortex scaffolds processing hierarchy

The human neocortex consists of tangentially organized layers with unique cytoarchitectural properties. These layers show spatial variations in thickness and cytoarchitecture across the neocortex, which is thought to support brain function through enabling targeted corticocortical connections. Here, leveraging maps of the six cortical layers in 3D human brain histology, we aimed to quantitatively characterize the systematic covariation of laminar structure in the cortex and its functional consequences. After correcting for the effect of cortical curvature, we identified a spatial pattern of changes in laminar thickness covariance from lateral frontal to posterior occipital regions, which differentiated the dominance of infra- versus supragranular layer thickness. Corresponding to the laminar regularities of cortical connections along cortical hierarchy, the infragranular-dominant pattern of laminar thickness was associated with higher hierarchical positions of regions, mapped based on resting-state effective connectivity in humans and tract-tracing of structural connections in macaques. Moreover, we show that regions with comparable laminar thickness patterns correspond to inter-regional structural covariance, maturational coupling, and transcriptomic patterning, indicating developmental relevance. In sum, here we characterize the association between organization of laminar thickness and processing hierarchy, anchored in ontogeny. As such, we illustrate how laminar organization may provide a foundational principle ultimately supporting human cognitive functioning.

neuroscience↗

bioRxiv2023

Brain functional characterization of response-code conflict in dual-tasking and its modulation by age

Crosstalk between conflicting response codes contributes to interference in dual-tasking, an effect exacerbated in advanced age. Here, we investigated (1) brain activity correlates of such response-code conflicts, (2) activity modulations by individual dual-task performance and related cognitive abilities, (3) task-modulated connectivity within the task network, and (4)age-related differences in all these aspects. Young and older adults underwent fMRI while responding to the pitch of tones through spatially mapped speeded button presses with one or two hands concurrently. Using opposing stimulus-response mappings between hands, we induced conflict between simultaneously activated response codes. These response-code conflicts elicited activation in key regions of the multiple-demand network. Older adults showed non-compensatory hyperactivity in left superior frontal gyrus, and higher left intraparietal sulcus activity associated with lower attentional performance. While motor and parietal areas of the conflict-related network were modulated by attentional and task-switching abilities, efficient conflict resolution in dual-tasking was linked to suppressing visual cortex activity. Finally, connectivity between premotor or parietal seed regions and the conflict-sensitive network was neither conflict-specific nor age-sensitive. Overall, resolving dual-task response-code conflict recruited substantial parts of the multiple-demand network, whose activity and coupling, however, were only little affected by individual differences in task performance or age.

neuroscience↗

bioRxiv2023

Primate Cerebellar Scaling in Connection to the Cerebrum: A 34-Species Phylogenetic Comparative Analysis

The cerebellum has increasingly been recognized for its role in diverse functional processes. The reciprocally connected cerebello-cerebral system may scaffold both brain size increase and advanced associative abilities, evolving highly coordinately in primates. In parallel, functional cerebello-cerebral modules have undergone reorganization and cerebellar lobules crura I-II (the ansiform area across mammals) have been reported to be specifically expanded in humans. Here we manually segmented 63 cerebella (34 primate species; 9 infraorders) and 30 crura I-II (13 species; 8 infraorders). We show that both constraints and reorganization may shape the evolution of the primate cerebello-cerebral system. Using phylogenetic generalized least squares, we find that the cerebellum scales isometrically with the cerebral cortex, whereas crura I-II scale hyper-allometrically versus both. Our phylogenetic analyses evidence primate-general crura I-II hyperscaling in contrast to virtually isometric cerebello-cerebral scaling. Crura I-II hyperscaling may be important for associative and cognitive brain functions in an evolutionary context.

evolutionary biology↗

bioRxiv2023

A Latent Clinical-anatomical Dimension Relating Metabolic Syndrome to Brain Morphology - Evidence from a Multivariate Imaging Analysis of 40,087 Individuals

The link between metabolic syndrome (MetS) and neurodegenerative as well cerebrovascular conditions holds substantial implications for brain health in at-risk populations. This study elucidates the complex relationship between MetS and brain health by conducting a comprehensive examination of cardiometabolic risk factors, cortical morphology, and cognitive function in 40,087 individuals. Multivariate, data-driven statistics identified a latent dimension linking more severe MetS to widespread brain morphological abnormalities, accounting for up to 71% of shared variance in the data. This dimension was replicable across sub-samples. In a mediation analysis we could demonstrate that MetS-related brain morphological abnormalities mediated the link between MetS severity and cognitive performance in multiple domains. Employing imaging transcriptomics and connectomics, our results also suggest that MetS-related morphological abnormalities are linked to the regional cellular composition and macroscopic brain network organization. By leveraging extensive, multi-domain data combined with a dimensional stratification approach, our analysis provides profound insights into the association of MetS and brain health. These findings can inform effective therapeutic and risk mitigation strategies aimed at maintaining brain integrity.

neuroscience↗

bioRxiv2023

The Burden of Reliability: How Measurement Noise Limits Brain-Behaviour Predictions

Major efforts in human neuroimaging strive to understand individual differences and find biomarkers for clinical applications by predicting behavioural phenotypes from brain imaging data. An essential prerequisite for identifying generalizable and replicable brain-behaviour prediction models is sufficient measurement reliability. However, the selection of prediction targets is predominantly guided by scientific interest or data availability rather than reliability considerations. Here we demonstrate the impact of low phenotypic reliability on out-of-sample prediction performance. Using simulated and empirical data from the Human Connectome Projects, we found that reliability levels common across many phenotypes can markedly limit the ability to link brain and behaviour. Next, using 5000 subjects from the UK Biobank, we show that only highly reliable data can fully benefit from increasing sample sizes from hundreds to thousands of participants. Overall, our findings highlight the importance of measurement reliability for identifying brain-behaviour associations from individual differences.

neuroscience↗

bioRxiv2023

A systematic comparison of VBM pipelines and their application to age prediction

Voxel-based morphometry (VBM) analysis is commonly used for localized quantification of gray matter volume (GMV). Several alternatives exist to implement a VBM pipeline. However, how these alternatives compare and their utility in applications, such as the estimation of aging effects, remain largely unclear. This leaves researchers wondering which VBM pipeline they should use for their project. In this study, we took a user-centric perspective and systematically compared five VBM pipelines, together with registration to either a general or a study-specific template, utilizing three large datasets (n>500 each). Considering the known effect of aging on GMV, we first compared the pipelines in their ability of individual-level age prediction and found markedly varied results. To examine whether these results arise from systematic differences between the pipelines, we classified them based on their GMVs, resulting in near-perfect accuracy. To gain deeper insights, we examined the impact of different VBM steps using the region-wise similarity between pipelines. The results revealed marked differences, largely driven by segmentation and registration steps. We observed large variability in subject-identification accuracies, highlighting the interpipeline differences in individual-level quantification of GMV. As a biologically meaningful criterion we correlated regional GMV with age. The results were in line with the age-prediction analysis, and two pipelines, CAT and the combination of fMRIPrep for tissue characterization with FSL for registration, reflected age information better.

neuroscience↗

bioRxiv2022

Brain-age prediction: a systematic comparison of machine learning workflows

The difference between age predicted using anatomical brain scans and chronological age, i.e., the brain-age delta, provides a proxy for atypical aging. Various data representations and machine learning (ML) algorithms have been used for brain-age estimation. However, how these choices compare on performance criteria important for real-world applications, such as; (1) within-site accuracy, (2) cross-site generalization, (3) test-retest reliability, and (4) longitudinal consistency, remains uncharacterized. We evaluated 128 workflows consisting of 16 feature representations derived from gray matter (GM) images and eight ML algorithms with diverse inductive biases. Using four large neuroimaging databases covering the adult lifespan (total N = 2953, 18-88 years), we followed a systematic model selection procedure by sequentially applying stringent criteria. The 128 workflows showed a within-site mean absolute error (MAE) between 4.73-8.38 years, from which 32 broadly sampled workflows showed a cross-site MAE between 5.23-8.98 years. The test-retest reliability and longitudinal consistency of the top 10 workflows were comparable. The choice of feature representation and the ML algorithm both affected the performance. Specifically, voxel-wise feature spaces (smoothed and resampled), with and without principal components analysis, with non-linear and kernel-based ML algorithms performed well. Strikingly, the correlation of brain-age delta with behavioral measures disagreed between within-site and cross-site predictions. Application of the best-performing workflow on the ADNI sample showed a significantly higher brain-age delta in Alzheimers and mild cognitive impairment patients. However, in the presence of age bias, the delta estimates in the diseased population varied depending on the sample used for bias correction. Taken together, brain-age shows promise, but further evaluation and improvements are needed for its real-world application. HighlightsO_LIThere is an effect of both feature space and ML algorithm on prediction error. C_LIO_LIVoxel-wise features performed better than parcel-wise features. C_LIO_LIGPR, KRR and RVR algorithms performed well. C_LIO_LIThe within-site and cross-site delta-behavior correlations disagree. C_LIO_LIHigher brain-age delta inference in AD depends on data used for bias correction. C_LI

neuroscience↗

bioRxiv2022

Homotopic local-global parcellation of the human cerebral cortex from resting-state functional connectivity

Resting-state fMRI is commonly used to derive brain parcellations, which are widely used for dimensionality reduction and interpreting human neuroscience studies. We previously developed a model that integrates local and global approaches for estimating areal-level cortical parcellations. The resulting local-global parcellations are often referred to as the Schaefer parcellations. However, the lack of homotopic correspondence between left and right Schaefer parcels has limited their use for brain lateralization studies. Here, we extend our previous model to derive homotopic areal-level parcellations. Using resting-fMRI and task-fMRI across diverse scanners, acquisition protocols, preprocessing and demographics, we show that the resulting homotopic parcellations are as homogeneous as the Schaefer parcellations, while being more homogeneous than five publicly available parcellations. Furthermore, weaker correlations between homotopic parcels are associated with greater lateralization in resting network organization, as well as lateralization in language and motor task activation. Finally, the homotopic parcellations agree with the boundaries of a number of cortical areas estimated from histology and visuotopic fMRI, while capturing sub-areal (e.g., somatotopic and visuotopic) features. Overall, these results suggest that the homotopic local- global parcellations represent neurobiologically meaningful subdivisions of the human cerebral cortex and will be a useful resource for future studies. Multi-resolution parcellations estimated from 1479 participants are publicly available (GITHUB_LINK).

neuroscience↗

bioRxiv2022

Intermediately Synchronised Brain States optimise trade-off between Subject Identifiability and Predictive Capacity

Functional connectivity (FC) refers to the statistical dependencies between activity of distinct brain areas. To study temporal fluctuations in FC within the duration of a functional magnetic resonance imaging (fMRI) scanning session, researchers have proposed the computation of an edge time series (ETS) and their derivatives. Evidence suggests that FC is driven by a few time points of high-amplitude co-fluctuation (HACF) in the ETS, which may also contribute disproportionately to interindividual differences. However, it remains unclear to what degree different time points actually contribute to brain-behaviour associations. Here, we systematically evaluate this question by assessing the predictive utility of FC estimates at different levels of co-fluctuation using machine learning (ML) approaches. We demonstrate that time points of lower and intermediate co-fluctuation levels provide overall highest subject specificity as well as highest predictive capacity of individual-level phenotypes.

neuroscience↗

bioRxiv2022

The Uniqueness of Human Vulnerability to Brain Aging in Great Ape Evolution

Aging is associated with robust decline of the brains gray matter. This spatially specific, morphological change in humans has recently been found in chimpanzees. Direct comparison of age-related brain deterioration between these great ape species can provide a unique evolutionary perspective on human brain aging. Here, we present a data-driven, cross-species comparative framework to explore the relationship between gray matter atrophy with age and cross-species cerebral expansion in chimpanzees and humans. In humans, we found a positive relationship between cerebral aging and cortical expansion, whereas, in chimpanzees no such relationship was found. The greater aging and expansion effects in higher-order cognitive regions like the orbito-frontal cortex were observed to be unique to humans. This resembles the last in, first out hypothesis for neurodevelopment and may represent a biological cost for recent evolutionary developments of human faculties.

neuroscience↗

bioRxiv2022

NEUROTRANSMITTER TRANSPORTER/RECEPTOR CO-EXPRESSION SHARES ORGANIZATIONAL TRAITS WITH BRAIN STRUCTURE AND FUNCTION

The relationship between brain areas based on neurotransmitter receptor and transporter molecule expression patterns may provide a link between brain structure and its function. Here, we studied the organization of the receptome, a measure of regional neurotransmitter receptor/transporter molecule (NTRM) similarity, derived from in vivo PET imaging studies of 19 different receptors and transporters. Nonlinear dimensionality reduction revealed three main spatial gradients of receptor similarity in the cortex. The first gradient differentiated the somato-motor network from the remaining cortex. The second gradient spanned between temporo-occipital and frontal anchors, differentiating visual and limbic networks from attention and control networks, and the third receptome gradient was anchored between the occipital and temporal cortices. In subcortical structures, the receptome delineated a striato-thalamic axis, separating functional communities. Moreover, we observed similar organizational principles underlying receptome differentiation in cortex and subcortex, indicating a link between subcortical and cortical NTRM patterning. Overall, we found that the cortical receptome shared key organizational traits with brain structure and function. Node-level correspondence of receptor similarity to functional, microstructural, and diffusion MRI-based measures decreased along a primary-to-transmodal gradient. Compared to primary and paralimbic regions, we observed higher receptomic diversification in unimodal and heteromodal regions, possibly supporting functional flexibility. In sum, we show how receptor similarity may form an additional organizational layer of human brain architecture, bridging brain structure and function.

neuroscience↗

bioRxiv2022

There is no fundamental trade-off between prediction accuracy and feature importance reliability

There is significant interest in using neuroimaging data to predict behavior. The predictive models are often interpreted by the computation of feature importance, which quantifies the predictive relevance of an imaging feature. Tian and Zalesky (2021) suggest that feature importance estimates exhibit low split-half reliability, as well as a trade-off between prediction accuracy and feature importance reliability across parcellation resolutions. However, it is unclear whether the trade-off between prediction accuracy and feature importance reliability is universal. Here, we demonstrate that, with a sufficient sample size, feature importance (operationalized as Haufe-transformed weights) can achieve fair to excellent split-half reliability. With a sample size of 2600 participants, Haufe-transformed weights achieve average intra-class correlation coefficients of 0.75, 0.57 and 0.53 for cognitive, personality and mental health measures respectively. Haufe-transformed weights are much more reliable than original regression weights and univariate FC-behavior correlations. Original regression weights are not reliable even with 2600 participants. Intriguingly, feature importance reliability is strongly positively correlated with prediction accuracy across phenotypes. Within a particular behavioral domain, there is no clear relationship between prediction performance and feature importance reliability across regression models. Furthermore, we show mathematically that feature importance reliability is necessary, but not sufficient, for low feature importance error. In the case of linear models, lower feature importance error is mathematically related to lower prediction error. Therefore, higher feature importance reliability might yield lower feature importance error and higher prediction accuracy. Finally, we discuss how our theoretical results relate with the reliability of imaging features and behavioral measures. Overall, the current study provides empirical and theoretical insights into the relationship between prediction accuracy and feature importance reliability.

neuroscience↗