Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A temporal decomposition method for identifying venous effects in task-based fMRI.

ABSTRACT: The spatial resolution of functional magnetic resonance imaging (fMRI) is fundamentally limited by effects from large draining veins. Here we describe an analysis method that provides data-driven estimates of these effects in task-based fMRI. The method involves fitting a one-dimensional manifold that characterizes variation in response timecourses observed in a given dataset, and then using identified early and late timecourses as basis functions for decomposing responses into components related to the microvasculature (capillaries and small venules) and the macrovasculature (large veins), respectively. We show the removal of late components substantially reduces the superficial cortical depth bias of fMRI responses and helps eliminate artifacts in cortical activity maps. This method provides insight into the origins of the fMRI signal and can be used to improve the spatial accuracy of fMRI.

SUBMITTER: Kay K

PROVIDER: S-EPMC7721302 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A temporal decomposition method for identifying venous effects in task-based fMRI.

Kay Kendrick K Jamison Keith W KW Zhang Ru-Yuan RY Uğurbil Kamil K

Nature methods 20200907 10

The spatial resolution of functional magnetic resonance imaging (fMRI) is fundamentally limited by effects from large draining veins. Here we describe an analysis method that provides data-driven estimates of these effects in task-based fMRI. The method involves fitting a one-dimensional manifold that characterizes variation in response timecourses observed in a given dataset, and then using identified early and late timecourses as basis functions for decomposing responses into components relate ...[more]

PMID: 32895538

Similar Datasets

Variance decomposition for single-subject task-based fMRI activity estimates across many sessions.

Project description:Here we report an exploratory within-subject variance decomposition analysis conducted on a task-based fMRI dataset with an unusually large number of repeated measures (i.e., 500 trials in each of three different subjects) distributed across 100 functional scans and 9 to 10 different sessions. Within-subject variance was segregated into four primary components: variance across-sessions, variance across-runs within a session, variance across-blocks within a run, and residual measurement/modeling error. Our results reveal inhomogeneous and distinct spatial distributions of these variance components across significantly active voxels in grey matter. Measurement error is dominant across the whole brain. Detailed evaluation of the remaining three components shows that across-session variance is the second largest contributor to total variance in occipital cortex, while across-runs variance is the second dominant source for the rest of the brain. Network-specific analysis revealed that across-block variance contributes more to total variance in higher-order cognitive networks than in somatosensory cortex. Moreover, in some higher-order cognitive networks across-block variance can exceed across-session variance. These results help us better understand the temporal (i.e., across blocks, runs and sessions) and spatial distributions (i.e., across different networks) of within-subject natural variability in estimates of task responses in fMRI. They also suggest that different brain regions will show different natural levels of test-retest reliability even in the absence of residual artifacts and sufficiently high contrast-to-noise measurements. Further confirmation with a larger sample of subjects and other tasks is necessary to ensure generality of these results.

| S-EPMC5398961 | biostudies-literature

Mode decomposition-based time-varying phase synchronization for fMRI.

Project description:Recently, there has been significant interest in measuring time-varying functional connectivity (TVC) between different brain regions using resting-state functional magnetic resonance imaging (rs-fMRI) data. One way to assess the relationship between signals from different brain regions is to measure their phase synchronization (PS) across time. However, this requires the a priori choice of type and cut-off frequencies for the bandpass filter needed to perform the analysis. Here we explore alternative approaches based on the use of various mode decomposition (MD) techniques that provide a more data driven solution to this issue. These techniques allow for the data driven decomposition of signals jointly into narrow-band components at different frequencies, thus fulfilling the requirements needed to measure PS. We explore several variants of MD, including empirical mode decomposition (EMD), bivariate EMD (BEMD), noise-assisted multivariate EMD (na-MEMD), and introduce the use of multivariate variational mode decomposition (MVMD) in the context of estimating time-varying PS. We contrast the approaches using a series of simulations and application to rs-fMRI data. Our results show that MVMD outperforms other evaluated MD approaches, and further suggests that this approach can be used as a tool to reliably investigate time-varying PS in rs-fMRI data.

| S-EPMC9451171 | biostudies-literature

A New Method of Identifying Characteristic Points in the Impedance Cardiography Signal Based on Empirical Mode Decomposition.

Project description:The accurate detection of fiducial points in the impedance cardiography signal (ICG) has a decisive impact on the proper estimation of diagnostic parameters such as stroke volume or cardiac output. It is, therefore, necessary to find an algorithm that is able to assess their positions with great precision. The solution to this problem is, however, quite challenging with regard to the high sensitivity of the ICG technique to the noise and varying morphology of the acquired signals. The aim of this study is to propose a novel method that allows us to overcome these limitations. The developed algorithm is based on Empirical Mode Decomposition (EMD)-an effective technique for processing and analyzing various types of non-stationary signals. We find high correlations between the results obtained from the algorithm and annotated by an expert. This, in turn, implies that the difference in estimation of the diagnostic-relevant parameters is small, which suggests that the method can automatically provide precise clinical information.

| S-EPMC9861967 | biostudies-literature

Task-based functional connectivity of the Useful Field of View (UFOV) fMRI task.

Project description:Declines in processing speed performance occur in aging and are a critical marker of functional independence in older adults. Numerous studies suggest that Useful Field of View (UFOV) training may ameliorate cognitive decline in older adults. Despite its efficacy, little is known about the neural correlates of this task. The current study is the first to investigate the coherence of functional connectivity during UFOV task completion. A total of 336 participants completed the UFOV task while undergoing task-based functional magnetic resonance imaging (fMRI). Ten spherical regions of interest (ROIs), selected a priori, were created based on regions with the greatest peak BOLD activation patterns in the UFOV fMRI task and regions that have been shown to significantly relate to UFOV fMRI task performance. We used a weighted ROI-to-ROI connectivity analysis to model task-specific functional connectivity strength between these a priori selected ROIs. We found that our UFOV fMRI network was functionally connected during task performance and was significantly associated to UFOV fMRI task performance. Within-network connectivity of the UFOV fMRI network showed comparable or better predictive power in accounting for UFOV accuracy compared to 7 resting state networks, delineated by Yeo and colleagues. Finally, we demonstrate that the within-network connectivity of UFOV fMRI task accounted for scores on a measure of "near transfer", the Double Decision task, better than the aforementioned resting state networks. Our data elucidate functional connectivity patterns of the UFOV fMRI task. This may assist in future targeted interventions that aim to improve synchronicity within the UFOV fMRI network.

| S-EPMC9886714 | biostudies-literature

A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes.

Project description:Identifying the genes involved in venous thromboembolism (VTE) recurrence is important not only for understanding the pathogenesis but also for discovering the therapeutic targets. We proposed a novel prioritization method called Function-Interaction-Pearson (FIP) by creating gene-disease similarity scores to prioritize candidate genes underling VTE. The scores were calculated by integrating and optimizing three types of resources including gene expression, gene ontology and protein-protein interaction. As a result, 124 out of top 200 prioritized candidate genes had been confirmed in literature, among which there were 34 antithrombotic drug targets. Compared with two well-known gene prioritization tools Endeavour and ToppNet, FIP was shown to have better performance. The approach provides a valuable alternative for drug targets discovery and disease therapy.

| S-EPMC4822849 | biostudies-literature

Functional correlates of cognitive performance and working memory in temporal lobe epilepsy: Insights from task-based and resting-state fMRI.

Project description:Temporal lobe epilepsy (TLE) is a common form of medically intractable epilepsy. Although seizures originate in mesial temporal structures, there are widespread abnormalities of gray and white matter beyond the temporal lobes that negatively impact functional networks and cognition. Previous studies have focused either on the global impact on functional networks, or on the functional correlates of specific cognitive abilities. Here, we use a two-pronged approach to evaluate the link between whole-brain functional connectivity (FC) anomalies to overall cognitive performance, and how such abnormal connectivity alters the fronto-parietal brain regions involved in working memory (WMem), a cognitive disability often reported by TLE patients. We evaluated 31 TLE patients and 35 healthy subjects through extensive cognitive testing, resting-state functional magnetic resonance imaging (RS-fMRI), and task-based fMRI using Sternberg's task to evaluate WMem. As a group, TLE patients displayed cognitive abnormalities across different domains, although considerable within-group variability was identified. TLE patients showed disruptions of functional networks between and within the default mode network (DMN) and task-positive networks (TPN) resulting in associations with cognitive performance. Furthermore, during the WMem task, TLE patients showed abnormal activity of fronto-parietal regions that were associated with other forms of memory, and alterations of seed-based connectivity analyses. Our results show that different degrees of abnormal functional brain activity and connectivity are related to the severity of disabilities across cognitive spheres. Differential co-activation patterns between patients and healthy subjects suggest potential compensatory mechanisms to preserve adequate cognitive performance.

| S-EPMC10936866 | biostudies-literature

Identifying drug-pathway association pairs based on L1L2,1-integrative penalized matrix decomposition.

Project description:The traditional methods of drug discovery follow the "one drug-one target" approach, which ignores the cellular and physiological environment of the action mechanism of drugs. However, pathway-based drug discovery methods can overcome this limitation. This kind of method, such as the Integrative Penalized Matrix Decomposition (iPaD) method, identifies the drug-pathway associations by taking the lasso-type penalty on the regularization term. Moreover, instead of imposing the L1-norm regularization, the L2,1-Integrative Penalized Matrix Decomposition (L2,1-iPaD) method imposes the L2,1-norm penalty on the regularization term. In this paper, based on the iPaD and L2,1-iPaD methods, we propose a novel method named L1L2,1-iPaD (L1L2,1-Integrative Penalized Matrix Decomposition), which takes the sum of the L1-norm and L2,1-norm penalties on the regularization term. Besides, we perform permutation test to assess the significance of the identified drug-pathway association pairs and compute the P-values. Compared with the existing methods, our method can identify more drug-pathway association pairs which have been validated in the CancerResource database. In order to identify drug-pathway associations which are not validated in the CancerResource database, we retrieve published papers to prove these associations. The results on two real datasets prove that our method can achieve better enrichment for identified association pairs than the iPaD and L2,1-iPaD methods.

| S-EPMC5564627 | biostudies-other

Simultaneous EEG-fMRI reveals a temporal cascade of task-related and default-mode activations during a simple target detection task.

Project description:Focused attention continuously and inevitably fluctuates, and to completely understand the mechanisms responsible for these modulations it is necessary to localize the brain regions involved. During a simple visual oddball task, neural responses measured by electroencephalography (EEG) modulate primarily with attention, but source localization of the correlates is a challenge. In this study we use single-trial analysis of simultaneously-acquired scalp EEG and functional magnetic resonance image (fMRI) data to investigate the blood oxygen level dependent (BOLD) correlates of modulations in task-related attention, and we unravel the temporal cascade of these transient activations. We hypothesize that activity in brain regions associated with various task-related cognitive processes modulates with attention, and that their involvements occur transiently in a specific order. We analyze the fMRI BOLD signal by first regressing out the variance linked to observed stimulus and behavioral events. We then correlate the residual variance with the trial-to-trial variation of EEG discriminating components for identical stimuli, estimated at a sequence of times during a trial. Post-stimulus and early in the trial, we find activations in right-lateralized frontal regions and lateral occipital cortex, areas that are often linked to task-dependent processes, such as attentional orienting, and decision certainty. After the behavioral response we see correlates in areas often associated with the default-mode network and introspective processing, including precuneus, angular gyri, and posterior cingulate cortex. Our results demonstrate that during simple tasks both task-dependent and default-mode networks are transiently engaged, with a distinct temporal ordering and millisecond timescale.

| S-EPMC3926909 | biostudies-literature

Nonlinear ICA of fMRI reveals primitive temporal structures linked to rest, task, and behavioral traits.

Project description:Accumulating evidence from whole brain functional magnetic resonance imaging (fMRI) suggests that the human brain at rest is functionally organized in a spatially and temporally constrained manner. However, because of their complexity, the fundamental mechanisms underlying time-varying functional networks are still not well understood. Here, we develop a novel nonlinear feature extraction framework called local space-contrastive learning (LSCL), which extracts distinctive nonlinear temporal structure hidden in time series, by training a deep temporal convolutional neural network in an unsupervised, data-driven manner. We demonstrate that LSCL identifies certain distinctive local temporal structures, referred to as temporal primitives, which repeatedly appear at different time points and spatial locations, reflecting dynamic resting-state networks. We also show that these temporal primitives are also present in task-evoked spatiotemporal responses. We further show that the temporal primitives capture unique aspects of behavioral traits such as fluid intelligence and working memory. These results highlight the importance of capturing transient spatiotemporal dynamics within fMRI data and suggest that such temporal primitives may capture fundamental information underlying both spontaneous and task-induced fMRI dynamics.

| S-EPMC7759729 | biostudies-literature

Dynamics of task-based confidence in schizophrenia using seasonal decomposition approach.

Project description:ObjectiveIntrospective Accuracy (IA) is a metacognitive construct that refers to alignment of self-generated accuracy judgments, confidence, and objective information regarding performance. IA not only refers to accuracy and confidence during tasks, but also predicts functional outcomes. The consistency and magnitude of IA deficits suggest a sustained disconnect between self-assessments and actual performance. The cognitive origins of IA are unclear and are not simply due to poor performance. We tried to capture task and diagnosis-related differences through examining confidence as a timeseries.MethodThis relatively large sample (N = 171; Bipolar = 71, Schizophrenia = 100) study used item by item confidence judgments for tasks including the Wisconsin Card Sorting Task (WCST) and the Emotion Recognition task (ER-40). Using a seasonal decomposition approach and AutoRegressive, Integrative and Moving Averages (ARIMA) time-series analyses we tested for the presence of randomness and perseveration.ResultsFor the WCST, comparisons across participants with schizophrenia and bipolar disorder found similar trends and residuals, thus excluding perseverative or random responding. However, seasonal components were weaker in participants with schizophrenia, reflecting a reduced impact of feedback on confidence. In contrast, for the ER40, which does not require identification of a sustained construct, seasonal, trend, and residual analyses were highly comparable.ConclusionSeasonal analysis revealed that confidence judgments in participants with schizophrenia on tasks requiring responses to feedback reflected diminished incorporation of external information, not random or preservative responding. These analyses highlight how time series analyses can specify potential faulty processes for future intervention.

| S-EPMC9883296 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data