Dataset Information

ICA-based artifact removal diminishes scan site differences in multi-center resting-state fMRI.

ABSTRACT: Resting-state fMRI (R-fMRI) has shown considerable promise in providing potential biomarkers for diagnosis, prognosis and drug response across a range of diseases. Incorporating R-fMRI into multi-center studies is becoming increasingly popular, imposing technical challenges on data acquisition and analysis, as fMRI data is particularly sensitive to structured noise resulting from hardware, software, and environmental differences. Here, we investigated whether a novel clean up tool for structured noise was capable of reducing center-related R-fMRI differences between healthy subjects. We analyzed three Tesla R-fMRI data from 72 subjects, half of whom were scanned with eyes closed in a Philips Achieva system in The Netherlands, and half of whom were scanned with eyes open in a Siemens Trio system in the UK. After pre-statistical processing and individual Independent Component Analysis (ICA), FMRIB's ICA-based X-noiseifier (FIX) was used to remove noise components from the data. GICA and dual regression were run and non-parametric statistics were used to compare spatial maps between groups before and after applying FIX. Large significant differences were found in all resting-state networks between study sites before using FIX, most of which were reduced to non-significant after applying FIX. The between-center difference in the medial/primary visual network, presumably reflecting a between-center difference in protocol, remained statistically significant. FIX helps facilitate multi-center R-fMRI research by diminishing structured noise from R-fMRI data. In doing so, it improves combination of existing data from different centers in new settings and comparison of rare diseases and risk genes for which adequate sample size remains a challenge.

SUBMITTER: Feis RA

PROVIDER: S-EPMC4621866 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

ICA-based artifact removal diminishes scan site differences in multi-center resting-state fMRI.

Feis Rogier A RA Smith Stephen M SM Filippini Nicola N Douaud Gwenaëlle G Dopper Elise G P EG Heise Verena V Trachtenberg Aaron J AJ van Swieten John C JC van Buchem Mark A MA Rombouts Serge A R B SA Mackay Clare E CE

Frontiers in neuroscience 20151027

Resting-state fMRI (R-fMRI) has shown considerable promise in providing potential biomarkers for diagnosis, prognosis and drug response across a range of diseases. Incorporating R-fMRI into multi-center studies is becoming increasingly popular, imposing technical challenges on data acquisition and analysis, as fMRI data is particularly sensitive to structured noise resulting from hardware, software, and environmental differences. Here, we investigated whether a novel clean up tool for structured ...[more]

PMID: 26578859

Similar Datasets

Project description:The identification of resting state networks (RSNs) and the quantification of their functional connectivity in resting-state fMRI (rfMRI) are seriously hindered by the presence of artefacts, many of which overlap spatially or spectrally with RSNs. Moreover, recent developments in fMRI acquisition yield data with higher spatial and temporal resolutions, but may increase artefacts both spatially and/or temporally. Hence the correct identification and removal of non-neural fluctuations is crucial, especially in accelerated acquisitions. In this paper we investigate the effectiveness of three data-driven cleaning procedures, compare standard against higher (spatial and temporal) resolution accelerated fMRI acquisitions, and investigate the combined effect of different acquisitions and different cleanup approaches. We applied single-subject independent component analysis (ICA), followed by automatic component classification with FMRIB's ICA-based X-noiseifier (FIX) to identify artefactual components. We then compared two first-level (within-subject) cleaning approaches for removing those artefacts and motion-related fluctuations from the data. The effectiveness of the cleaning procedures was assessed using time series (amplitude and spectra), network matrix and spatial map analyses. For time series and network analyses we also tested the effect of a second-level cleaning (informed by group-level analysis). Comparing these approaches, the preferable balance between noise removal and signal loss was achieved by regressing out of the data the full space of motion-related fluctuations and only the unique variance of the artefactual ICA components. Using similar analyses, we also investigated the effects of different cleaning approaches on data from different acquisition sequences. With the optimal cleaning procedures, functional connectivity results from accelerated data were statistically comparable or significantly better than the standard (unaccelerated) acquisition, and, crucially, with higher spatial and temporal resolution. Moreover, we were able to perform higher dimensionality ICA decompositions with the accelerated data, which is very valuable for detailed network analyses.

Project description:BackgroundArtifacts contained in EEG recordings hamper both, the visual interpretation by experts as well as the algorithmic processing and analysis (e.g. for Brain-Computer Interfaces (BCI) or for Mental State Monitoring). While hand-optimized selection of source components derived from Independent Component Analysis (ICA) to clean EEG data is widespread, the field could greatly profit from automated solutions based on Machine Learning methods. Existing ICA-based removal strategies depend on explicit recordings of an individual's artifacts or have not been shown to reliably identify muscle artifacts.MethodsWe propose an automatic method for the classification of general artifactual source components. They are estimated by TDSEP, an ICA method that takes temporal correlations into account. The linear classifier is based on an optimized feature subset determined by a Linear Programming Machine (LPM). The subset is composed of features from the frequency-, the spatial- and temporal domain. A subject independent classifier was trained on 640 TDSEP components (reaction time (RT) study, n = 12) that were hand labeled by experts as artifactual or brain sources and tested on 1080 new components of RT data of the same study. Generalization was tested on new data from two studies (auditory Event Related Potential (ERP) paradigm, n = 18; motor imagery BCI paradigm, n = 80) that used data with different channel setups and from new subjects.ResultsBased on six features only, the optimized linear classifier performed on level with the inter-expert disagreement (<10% Mean Squared Error (MSE)) on the RT data. On data of the auditory ERP study, the same pre-calculated classifier generalized well and achieved 15% MSE. On data of the motor imagery paradigm, we demonstrate that the discriminant information used for BCI is preserved when removing up to 60% of the most artifactual source components.ConclusionsWe propose a universal and efficient classifier of ICA components for the subject independent removal of artifacts from EEG data. Based on linear methods, it is applicable for different electrode placements and supports the introspection of results. Trained on expert ratings of large data sets, it is not restricted to the detection of eye- and muscle artifacts. Its performance and generalization ability is demonstrated on data of different EEG studies.

Project description:UNLABELLED:Functional magnetic resonance imaging (fMRI) studies have revealed the existence of robust, interconnected brain networks exhibiting correlated low frequency fluctuations during rest, which can be derived by examining inherent spatio-temporal patterns in functional scans independent of any a priori model. In order to explore the electrophysiological underpinnings of these networks, analogous techniques have recently been applied to magnetoencephalography (MEG) data, revealing similar networks that exhibit correlated low frequency fluctuations in the power envelope of beta band (14-30Hz) power. However, studies to date using this technique have concentrated on healthy subjects, and no method has yet been presented for group comparisons. We extended the ICA resting state MEG method to enable group comparisons, and demonstrate the technique in a sample of subjects with major depressive disorder (MDD). We found that the intrinsic resting state networks evident in fMRI appeared to be disrupted in individuals with MDD compared to healthy participants, particularly in the subgenual cingulate, although the electrophysiological correlates of this are unknown. Networks extracted from a combined group of healthy and MDD participants were examined for differences between groups. Individuals with MDD showed reduced correlations between the subgenual anterior cingulate (sgACC) and hippocampus in a network with primary nodes in the precentral and middle frontal gyri. Individuals with MDD also showed increased correlations between insulo-temporal nodes and amygdala compared to healthy controls. To further support our methods and findings, we present test/re-test reliability on independent recordings acquired within the same session. Our results demonstrate that group analyses are possible with the resting state MEG-independent component analysis (ICA) technique, highlighting a new pathway for analysis and discovery. This study also provides the first evidence of altered sgACC connectivity with a motor network. This finding, reliable across multiple sessions, suggests that the sgACC may partially mediate the psychomotor symptoms of MDD via synchronized changes in beta-band power, and expands the idea of the sgACC as a hub region mediating cognitive and emotional symptomatic domains in MDD. Findings of increased connectivity between the amygdala and cortical nodes further support the role of amygdalar networks in mediated depressive symptomatology. CLINICAL TRIALS IDENTIFIER:NCT00024635 (ZIA-MH002927-04).

Dataset Information

ICA-based artifact removal diminishes scan site differences in multi-center resting-state fMRI.

Publications

ICA-based artifact removal diminishes scan site differences in multi-center resting-state fMRI.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets