fMRI Independent Component Analysis Research Articles

Consistency of independent component analysis for FMRI

BackgroundIndependent component analysis (ICA) has been widely used for blind source separation in the field of medical imaging. However, despite of previous substantial efforts, the stability of ICA components remains a critical issue which has not been adequately addressed, despite numerous previous efforts. Most critical is the inconsistency of some of the extracted components when ICA is run with different model orders (MOs). New MethodIn this study, a novel method of determining the consistency of component analysis (CoCA) is proposed to evaluate the consistency of extracted components with different model orders. In the method, “consistent components” (CCs) are defined as those which can be extracted repeatably over a range of model orders. ResultThe efficacy of the method was evaluated with simulation data and fMRI datasets. With our method, the simulation result showed a clear difference of consistency between ground truths and noise. Comparison with existing methodsThe information criteria were implemented to provide suggestions for the optimal model order, where some of the ICs were revealed inconsistent in our proposed method. ConclusionsThis method provided an objective protocol for choosing CCs of an ICA decomposition of a data matrix, independent of model order. This is especially useful with high model orders, where noise or other disturbances could possibly lead to an instability of the components.

Thalamic connectivity measured with fMRI is associated with a polygenic index predicting thalamo-prefrontal gene co-expression.

The functional connectivity between thalamic medio-dorsal nucleus (MD) and cortical regions, especially the dorsolateral prefrontal cortex (DLPFC), is implicated in attentional processing and is anomalous in schizophrenia, a brain disease associated with polygenic risk and attentional deficits. However, the molecular and genetic underpinnings of thalamic connectivity anomalies are unclear. Given that gene co-expression across brain areas promotes synchronous interregional activity, our aim was to investigate whether coordinated expression of genes relevant to schizophrenia in MD and DLPFC may reflect thalamic connectivity anomalies in an attention-related network including the DLPFC. With this aim, we identified in datasets of post-mortem prefrontal mRNA expression from healthy controls a gene module with robust overrepresentation of genes with coordinated MD-DLPFC expression and enriched for schizophrenia genes according to the largest genome-wide association study to date. To link this gene cluster with imaging phenotypes, we computed a Polygenic Co-Expression Index (PCI) combining single-nucleotide polymorphisms predicting module co-expression. Finally, we investigated the association between PCI and thalamic functional connectivity during attention through fMRI Independent Component Analysis in 265 healthy participants. We found that PCI was positively associated with connectivity strength of a thalamic region overlapping with the MD within an attention brain circuit. These findings identify a novel association between schizophrenia-related genes and thalamic functional connectivity. Furthermore, they highlight the association between gene expression co-regulation and brain connectivity, such that genes with coordinated MD-DLPFC expression are associated with coordinated activity between the same brain regions. We suggest that gene co-expression is a plausible mechanism underlying biological phenotypes of schizophrenia.

Effect of Spatial Smoothing on Task fMRI ICA and Functional Connectivity.

Spatial smoothing is a widely used preprocessing step in functional magnetic resonance imaging (fMRI) data analysis. In this work, we report on the spatial smoothing effect on task-evoked fMRI brain functional mapping and functional connectivity. Initially, we decomposed the task fMRI data into a collection of components or networks by independent component analysis (ICA). The designed task paradigm helps identify task-modulated ICA components (highly correlated with the task stimuli). For the ICA-extracted primary task component, we then measured the task activation volume at the task response foci. We used the task timecourse (designed) as a reference to order the ICA components according to the task correlations of the ICA timecourses. With the re-ordered ICA components, we calculated the inter-component function connectivity (FC) matrix (correlations among the ICA timecourses). By repeating the spatial smoothing of fMRI data with a Gaussian smoothing kernel with a full width at half maximum (FWHM) of {1, 3, 6, 9, 12, 15, 20, 25, 30, 35} mm, we measured the spatial smoothing effects. Our results show spatial smoothing reveals the following effects: (1) It decreases the task extraction performance of single-subject ICA more than that of multi-subject ICA; (2) It increases the task volume of multi-subject ICA more than that of single-subject ICA; (3) It strengthens the functional connectivity of single-subject ICA more than that of multi-subject ICA; and (4) It impacts the positive-negative imbalance of single-subject ICA more than that of multi-subject ICA. Our experimental results suggest a 2~3 voxel FWHM spatial smoothing for single-subject ICA in achieving an optimal balance of functional connectivity, and a wide range (2~5 voxels) of FWHM for multi-subject ICA.

The mirror neuron system also rests.

The mirror neuron system (MNS) is a brain network that has been associated with the understanding of the actions performed by others. The main areas of the brain that are considered as belonging to the MNS are the rostral part of the inferior parietal lobe (IPL) and the inferior frontal gyrus (IFG). Many studies have tried to focus on the relationship between the regions belonging to the MNS, but a little consideration has been given to the study of the MNS in resting conditions. In the present experiment, the MNS has been studied by two fMRI modalities (task-based fMRI and resting-fMRI) and three analytical procedures [task-block comparison, functional connectivity (FC), and independent component analysis (ICA)]. The task-fMRI with block design showed a mirror activity located in the rostral IPL. The coordinates of this local maximum voxel were defined as a region of interest (ROI) for an FC analysis of the resting-fMRI. This analysis revealed the existence of a functional connectivity within regions forming the core of MNS network and also with other regions with mirror properties. Finally, resting-state fMRI ICA showed the same functional network, although it was more restricted to the core MNS regions. To the best of our knowledge, this is the first study that approaches the MNS using the resting-state fMRI analysis using independent component analysis and functional connectivity at the same time.

Building an EEG-fMRI Multi-Modal Brain Graph: A Concurrent EEG-fMRI Study.

The topological architecture of brain connectivity has been well-characterized by graph theory based analysis. However, previous studies have primarily built brain graphs based on a single modality of brain imaging data. Here we develop a framework to construct multi-modal brain graphs using concurrent EEG-fMRI data which are simultaneously collected during eyes open (EO) and eyes closed (EC) resting states. FMRI data are decomposed into independent components with associated time courses by group independent component analysis (ICA). EEG time series are segmented, and then spectral power time courses are computed and averaged within 5 frequency bands (delta; theta; alpha; beta; low gamma). EEG-fMRI brain graphs, with EEG electrodes and fMRI brain components serving as nodes, are built by computing correlations within and between fMRI ICA time courses and EEG spectral power time courses. Dynamic EEG-fMRI graphs are built using a sliding window method, versus static ones treating the entire time course as stationary. In global level, static graph measures and properties of dynamic graph measures are different across frequency bands and are mainly showing higher values in eyes closed than eyes open. Nodal level graph measures of a few brain components are also showing higher values during eyes closed in specific frequency bands. Overall, these findings incorporate fMRI spatial localization and EEG frequency information which could not be obtained by examining only one modality. This work provides a new approach to examine EEG-fMRI associations within a graph theoretic framework with potential application to many topics.

Differential functional brain network connectivity during visceral interoception as revealed by independent component analysis of fMRI TIME-series.

Influential theories of brain-viscera interactions propose a central role for interoception in basic motivational and affective feeling states. Recent neuroimaging studies have underlined the insula, anterior cingulate, and ventral prefrontal cortices as the neural correlates of interoception. However, the relationships between these distributed brain regions remain unclear. In this study, we used spatial independent component analysis (ICA) and functional network connectivity (FNC) approaches to investigate time course correlations across the brain regions during visceral interoception. Functional magnetic resonance imaging (fMRI) was performed in thirteen healthy females who underwent viscerosensory stimulation of bladder as a representative internal organ at different prefill levels, i.e., no prefill, low prefill (100 ml saline), and high prefill (individually adapted to the sensations of persistent strong desire to void), and with different infusion temperatures, i.e., body warm (∼37°C) or ice cold (4-8°C) saline solution. During Increased distention pressure on the viscera, the insula, striatum, anterior cingulate, ventromedial prefrontal cortex, amygdalo-hippocampus, thalamus, brainstem, and cerebellar components showed increased activation. A second group of components encompassing the insula and anterior cingulate, dorsolateral prefrontal and posterior parietal cortices and temporal-parietal junction showed increased activity with innocuous temperature stimulation of bladder mucosa. Significant differences in the FNC were found between the insula and amygdalo-hippocampus, the insula and ventromedial prefrontal cortex, and the ventromedial prefrontal cortex and temporal-parietal junction as the distention pressure on the viscera increased. These results provide new insight into the supraspinal processing of visceral interoception originating from an internal organ.

The effects of pediatric epilepsy on a language connectome.

This study introduces a new approach for assessing the effects of pediatric epilepsy on a language connectome. Two novel data-driven network construction approaches are presented. These methods rely on connecting different brain regions using either extent or intensity of language related activations as identified by independent component analysis of fMRI. An auditory word definition decision task paradigm was used to activate the language network for 29 patients and 30 controls. Evaluations illustrated that pediatric epilepsy is associated with a network efficiency reduction. Patients showed a propensity to inefficiently use the whole brain network to perform the language task; whereas, controls seemed to efficiently use smaller segregated network components to achieve the same task. To explain the causes of the decreased efficiency, graph theoretical analysis was performed. The analysis revealed substantial global network feature differences between the patients and controls for the extent of activation network. It also showed that for both subject groups the language network exhibited small-world characteristics; however, the patient's extent of activation network showed a tendency toward randomness. It was also shown that the intensity of activation network displayed ipsilateral hub reorganization on the local level. We finally showed that a clustering scheme was able to fairly separate the subjects into their respective patient or control groups. The clustering was initiated using local and global nodal measurements. Compared to the intensity of activation network, the extent of activation network clustering demonstrated better precision. This ascertained that the network differences presented by the networks were associated with pediatric epilepsy.

ICA Extracts Epileptic Sources from fMRI in EEG-Negative Patients: A Retrospective Validation Study

Simultaneous EEG-fMRI has proven to be useful in localizing interictal epileptic activity. However, the applicability of traditional GLM-based analysis is limited as interictal spikes are often not seen on the EEG inside the scanner. Therefore, we aim at extracting epileptic activity purely from the fMRI time series using independent component analysis (ICA). To our knowledge, we show for the first time that ICA can find sources related to epileptic activity in patients where no interictal spikes were recorded in the EEG. The epileptic components were identified retrospectively based on the known localization of the ictal onset zone (IOZ). We demonstrate that the selected components truly correspond to epileptic activity, as sources extracted from patients resemble significantly better the IOZ than sources found in healthy controls. Furthermore, we show that the epileptic components in patients with and without spikes recorded inside the scanner resemble the IOZ in the same degree. We conclude that ICA of fMRI has the potential to extend the applicability of EEG-fMRI for presurgical evaluation in epilepsy.

Multisubject Independent Component Analysis of fMRI: A Decade of Intrinsic Networks, Default Mode, and Neurodiagnostic Discovery

Since the discovery of functional connectivity in fMRI data (i.e., temporal correlations between spatially distinct regions of the brain) there has been a considerable amount of work in this field. One important focus has been on the analysis of brain connectivity using the concept of networks instead of regions. Approximately ten years ago, two important research areas grew out of this concept. First, a network proposed to be "a default mode of brain function" since dubbed the default mode network was proposed by Raichle. Secondly, multisubject or group independent component analysis (ICA) provided a data-driven approach to study properties of brain networks, including the default mode network. In this paper, we provide a focused review of how ICA has contributed to the study of intrinsic networks. We discuss some methodological considerations for group ICA and highlight multiple analytic approaches for studying brain networks. We also show examples of some of the differences observed in the default mode and resting networks in the diseased brain. In summary, we are in exciting times and still just beginning to reap the benefits of the richness of functional brain networks as well as available analytic approaches.

Segregation of frontoparietal and cerebellar components within saccade and vergence networks using hierarchical independent component analysis of fMRI

Cortical and subcortical functional activity stimulated via saccade and vergence eye movements were investigated to examine the similarities and differences between networks and regions of interest (ROIs). Blood oxygenation level-dependent (BOLD) signals from stimulus-induced functional Magnetic Resonance Imaging (MRI) experiments were analyzed studying 16 healthy subjects. Six types of oculomotor experiments were conducted using a block design to study both saccade and vergence circuits. The experiments included a simple eye movement task and a more cognitively demanding prediction task. A hierarchical independent component analysis (ICA) process began by analyzing individual subject data sets with spatial ICA to extract spatial independent components (sIC), which resulted in three ROIs. Using the time series from each of the three ROIs per subject, per oculomotor experiment, a temporal ICA was used to compute individual temporal independent components (tICs). For each of the three ROIs, the individual tICs from multiple subjects were entered into a second temporal ICA to compute group-level tICs for comparison. Two independent spatial maps were observed for each subject (one sIC showing activity in the frontoparietal regions and another sIC in the cerebellum) during the six oculomotor tasks. Analysis of group-level tICs revealed an increased latency in the cerebellar region when compared to the frontoparietal region. Shared neuronal behavior has been reported in the frontal and parietal lobes, which may in part explain the segregation of frontoparietal functional activity into one sIC. The cerebellum uses multiple time scales for motor learning. This may result in an increased latency observed in the BOLD signal of the cerebellar group-level tIC when compared to the frontal and parietal group-level tICs. The increased latency offers a possible explanation to why ICA dissects the cerebellar activity into an sIC. The hierarchical ICA process used to calculate group-level tICs can yield insight into functional connectivity within complex neural networks.

Maladaptive changes in event related brain activity preceding erroneous behavior

Event Abstract Back to Event Maladaptive changes in event related brain activity preceding erroneous behavior Tom Eichele1* 1 University of Bergen, Norway Recent EEG and fMRI evidence suggests that behavioral errors are foreshadowed by systematic changes in brain activity preceding the outcome by seconds. We have employed independent component analysis of fMRI and EEG data followed by deconvolution to investigate pre-error brain activity on a trial-by-trial basis. In fMRI data from a flanker and a Simon task we found that a coincident decrease of deactivation in default mode regions of the brain, together with a decline of task-related activation in posterior medial frontal and anterior insular regions. In addition to these changes that appear to be related to general maintenance of task effort we found in a further experiment that, prior to errors, activity in perceptual areas was systematically shifted away from the task-relevant features towards task-irrelevant stimulus features. In two additional large-sample EEG studies in which predictability of trial types in a flanker task was varied we observed gradual decrease of N2 amplitudes over multiple trials prior to errors that corroborate the fMRI findings. In sum, brain activity prior to errors reflects a number of parallel adaptive processes that may result in failure when overly active: (1) Increased subjective predictability of events reduces invested effort and performance monitoring activity. (2) Attention may adaptively shift towards irrelevant features of perceptual inputs that transiently predict the required response. (3) Reduced task-related effort allows for increased task-unrelated brain activity reflected in default mode network activity. In sum, this shift of net activity raises the likelihood of future errors. Keywords: EEG, fMRI, N2, neural activity Conference: XI International Conference on Cognitive Neuroscience (ICON XI), Palma, Mallorca, Spain, 25 Sep - 29 Sep, 2011. Presentation Type: Symposium: Oral Presentation Topic: Symposium 8: Preludes to failure: electrophysiological and hemodynamic antecedents of human error Citation: Eichele T (2011). Maladaptive changes in event related brain activity preceding erroneous behavior. Conference Abstract: XI International Conference on Cognitive Neuroscience (ICON XI). doi: 10.3389/conf.fnhum.2011.207.00518 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 09 Nov 2011; Published Online: 28 Nov 2011. * Correspondence: Dr. Tom Eichele, University of Bergen, Bergen, Norway, tom.eichele@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Tom Eichele Google Tom Eichele Google Scholar Tom Eichele PubMed Tom Eichele Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Imaging haemodynamic changes related to seizures: Comparison of EEG-based general linear model, independent component analysis of fMRI and intracranial EEG

BackgroundSimultaneous EEG-fMRI can reveal haemodynamic changes associated with epileptic activity which may contribute to understanding seizure onset and propagation. MethodsNine of 83 patients with focal epilepsy undergoing pre-surgical evaluation had seizures during EEG-fMRI and analysed using three approaches, two based on the general linear model (GLM) and one using independent component analysis (ICA):1.EEGs were divided into up to three phases: early ictal EEG change, clinical seizure onset and late ictal EEG change and convolved with a canonical haemodynamic response function (HRF) (canonical GLM analysis).2.Seizures lasting three scans or longer were additionally modelled using a Fourier basis set across the entire event (Fourier GLM analysis).3.Independent component analysis (ICA) was applied to the fMRI data to identify ictal BOLD patterns without EEG.The results were compared with intracranial EEG. ResultsThe canonical GLM analysis revealed significant BOLD signal changes associated with seizures on EEG in 7/9 patients, concordant with the seizure onset zone in 4/7. The Fourier GLM analysis revealed changes in BOLD signal corresponding with the results of the canonical analysis in two patients. ICA revealed components spatially concordant with the seizure onset zone in all patients (8/9 confirmed by intracranial EEG). ConclusionIctal EEG-fMRI visualises plausible seizure related haemodynamic changes. The GLM approach to analysing EEG-fMRI data reveals localised BOLD changes concordant with the ictal onset zone when scalp EEG reflects seizure onset. ICA provides additional information when scalp EEG does not accurately reflect seizures and may give insight into ictal haemodynamics.

A group model for stable multi-subject ICA on fMRI datasets

Spatial Independent Component Analysis (ICA) is an increasingly used data-driven method to analyze functional Magnetic Resonance Imaging (fMRI) data. To date, it has been used to extract sets of mutually correlated brain regions without prior information on the time course of these regions. Some of these sets of regions, interpreted as functional networks, have recently been used to provide markers of brain diseases and open the road to paradigm-free population comparisons. Such group studies raise the question of modeling subject variability within ICA: how can the patterns representative of a group be modeled and estimated via ICA for reliable inter-group comparisons?In this paper, we propose a hierarchical model for patterns in multi-subject fMRI datasets, akin to mixed-effect group models used in linear-model-based analysis. We introduce an estimation procedure, CanICA (Canonical ICA), based on i) probabilistic dimension reduction of the individual data, ii) canonical correlation analysis to identify a data subspace common to the group iii) ICA-based pattern extraction. In addition, we introduce a procedure based on cross-validation to quantify the stability of ICA patterns at the level of the group. We compare our method with state-of-the-art multi-subject fMRI ICA methods and show that the features extracted using our procedure are more reproducible at the group level on two datasets of 12 healthy controls: a resting-state and a functional localizer study.

Semi-blind ICA of fMRI: A method for utilizing hypothesis-derived time courses in a spatial ICA analysis

Independent component analysis (ICA) is a data-driven approach utilizing high-order statistical moments to find maximally independent sources that has found fruitful application in functional magnetic resonance imaging (fMRI). Being a blind source separation technique, ICA does not require any explicit constraints upon the fMRI time courses. However, for some fMRI data analysis applications, such as for the analysis of an event-related paradigm, it would be useful to flexibly incorporate paradigm information into the ICA analysis. In this paper, we present an approach for constrained or semi-blind ICA (sbICA) analysis of event-related fMRI data by imposing regularization on certain estimated time courses using the paradigm information. We demonstrate the performance of our approach using both simulations and fMRI data from a three-stimulus auditory oddball paradigm. Simulation results suggest that (1) a regression approach slightly outperforms ICA when prior information is accurate and ICA outperforms the general linear model (GLM)-based approach when prior information is not completely accurate, (2) prior information improves the robustness of ICA in the presence of noise, and (3) ICA analysis using prior information with temporal constraints can outperform a regression approach when the prior information is not completely accurate. Using fMRI data, we compare a regression-based conjunction analysis of target and novel stimuli, both of which elicit an orienting response, to an sbICA approach utilizing both the target and novel stimuli to constrain the ICA time courses. Results show similar positive associations for both GLM and sbICA, but sbICA detects additional negative associates consistent with regions implicated in a default mode of brain activity. This suggests that task-related default mode decreases have a more “complex” signal that benefits from a flexible modeling approach. Compared with a traditional GLM approach, the sbICA approach provides a flexible way to analyze fMRI data that reduces the assumptions placed upon the hemodynamic response of the brain. The advantages and limitations of our technique are discussed in detail in the manuscript to provide guidelines to the reader for developing useful applications. The use of prior time course information in a spatial ICA analysis, which combines elements of both a regression approach and a blind ICA approach, may prove to be a useful tool for fMRI analysis.

Latency (in)sensitive ICA: Group independent component analysis of fMRI data in the temporal frequency domain

Independent component analysis (ICA), a data-driven approach utilizing high-order statistical moments to find maximally independent sources, has found fruitful application in functional magnetic resonance imaging (fMRI). A limitation of the standard fMRI ICA model is that a given component's time course is required to have the same delay at every voxel. As spatially varying delays (SVDs) may be found in fMRI data, using an ICA model with a fixed temporal delay for each source will have two implications. Larger SVDs can result in the splitting of regions with different delays into different components. Second, smaller SVDs can result in a biased ICA amplitude estimate due to only a slight delay difference. We propose a straightforward approach for incorporating this prior temporal information and removing the limitation of a fixed source delay by performing ICA on the amplitude spectrum of the original fMRI data (thus removing latency information). A latency map is then estimated for each component using the resulting component images and the raw data. We show that voxels with similar time courses, but different delays, are grouped into the same component. Additionally, when using traditional ICA, the amplitudes of motor areas are diminished due to systematic delay differences between visual and motor areas. The amplitudes are more accurately estimated when using a latency-insensitive ICA approach. The resulting time courses, the component maps, and the latency maps may prove useful as an addition to the collection of methods for fMRI data analysis.

Modes or models: a critique on independent component analysis for fMRI

I thank Chris Frith for his invaluable comments. K.J.F. is supported by the Wellcome Trust.