Independent component analysis: a reliable alternative to general linear model for task-based fMRI (original) (raw)
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2008 2nd International Conference on Bioinformatics and Biomedical Engineering, 2008
Functional magnetic resonance imaging (fMRI) has been used to lateralize and localize language areas for pre-operative planning purposes. To identify the essential language areas from this kind of observation method, we propose an analysis strategy to combine fMRI data from two different tasks using probabilistic independent component analysis (PICA). The assumption is that the independent components separated by PICA identify the networks activated by both tasks. The results from a study of twelve normal subjects showed that a language-specific component was consistently identified, with the participating networks separated into different components. Compared with a model-based method, PICA's ability to capture the neural networks whose temporal activity may deviate from the task timing suggests that PICA may be more appropriate for analyzing language fMRI data with complex event-related paradigms, and may be particularly helpful for patient studies. This proposed strategy has the potential to improve the correlation between fMRI and invasive techniques which can demonstrate essential areas and which remain the clinical gold standard.
Applying Independent Component Analysis to Clinical fMRI at 7 T
Frontiers in Human Neuroscience, 2013
Increased BOLD sensitivity at 7T offers the possibility to increase the reliability of fMRI, but ultra-high field is also associated with an increase in artifacts related to head motion, Nyquist ghosting, and parallel imaging reconstruction errors. In this study, the ability of independent component analysis (ICA) to separate activation from these artifacts was assessed in a 7T study of neurological patients performing chin and hand motor tasks. ICA was able to isolate primary motor activation with negligible contamination by motion effects. The results of General Linear Model (GLM) analysis of these data were, in contrast, heavily contaminated by motion. Secondary motor areas, basal ganglia, and thalamus involvement were apparent in ICA results, but there was low capability to isolate activation in the same brain regions in the GLM analysis, indicating that ICA was more sensitive as well as more specific. A method was developed to simplify the assessment of the large number of independent components. Task-related activation components could be automatically identified via these intuitive and effective features. These findings demonstrate that ICA is a practical and sensitive analysis approach in high field fMRI studies, particularly where motion is evoked. Promising applications of ICA in clinical fMRI include presurgical planning and the study of pathologies affecting subcortical brain areas.
Statistical Analysis of Functional MRI Data using Independent Component Analysis
Functional magnetic resonance imaging (fMRI) is a technique to map the brain, anatomically as well as physiologically, which does not require any invasive analysis. In order to obtain brain activation maps, the subject under study must perform a task or be exposed to an external stimulus. At the same time a large amount of images are acquired using ultra-fast sequences through magnetic resonance. Afterwards, these images are processed and analyzed with statistical algorithms. This study was made in collaboration with the consolidated Neuropsychology Research Group of the University of Barcelona, focusing on applications of fMRI for the study of brain function in images obtained with various subjects. This group performed a study which analyzed fMRI data, acquired with various subjects, using the General Linear Model (GLM). The aim of our work was to analyze the same fMRI data using Independent Component Analysis (ICA) and compare the results with those obtained through GLM. Results showed that ICA was able to find more active networks than GLM. The activations were found in frontal, parietal, occipital and temporal areas.
American Journal of Neuroradiology, 2016
BACKGROUND AND PURPOSE: Although it is a potentially powerful presurgical tool, fMRI can be fraught with artifacts, leading to interpretive errors, many of which are not fully accounted for in routinely applied correction methods. The purpose of this investigation was to evaluate the effects of data denoising by independent component analysis in patients undergoing preoperative evaluation for glioma resection compared with more routinely applied correction methods such as realignment or motion scrubbing. MATERIALS AND METHODS: Thirty-five functional runs (both motor and language) in 12 consecutive patients with glioma were analyzed retrospectively by double-blind review. Data were processed and compared with the following: 1) realignment alone, 2) motion scrubbing, 3) independent component analysis denoising, and 4) both independent component analysis denoising and motion scrubbing. Primary outcome measures included a change in false-positives, false-negatives, z score, and diagnostic rating. RESULTS: Independent component analysis denoising reduced false-positives in 63% of studies versus realignment alone. There was also an increase in the z score in areas of true activation in 71.4% of studies. Areas of new expected activation (previous false-negatives) were revealed in 34.4% of cases with independent component analysis denoising versus motion scrubbing or realignment alone. Of studies deemed nondiagnostic with realignment or motion scrubbing alone, 65% were considered diagnostic after independent component analysis denoising. CONCLUSIONS: The addition of independent component analysis denoising of fMRI data in preoperative patients with glioma has a significant impact on data quality, resulting in reduced false-positives and an increase in true-positives compared with more commonly applied motion scrubbing or simple realignment methods. ABBREVIATIONS: BOLD ϭ blood oxygen level-dependent; ICA ϭ independent component analysis; DVARS ϭ root-mean-square of the derivatives of the differentiated time courses of every brain voxel for each acquired volume; MD ϭ mean displacement; TC ϭ task correlation
Independent component analysis of fMRI data: examining the assumptions
1998
Independent component analysis (ICA), which separates fMRI data into spatially independent patterns of activity, has recently been shown to be a suitable method for exploratory fMRI analysis. The validity of the assumptions of ICA, mainly that the underlying components are spatially independent and add linearly, was explored with a representative fMRI data set by calculating the log-likelihood of observing each voxel's time course conditioned on the ICA model. The probability of observing the time courses from white-matter voxels was higher compared to other observed brain regions. Regions containing blood vessels had the lowest probabilities. The statistical distribution of probabilities over all voxels did not resemble that expected for a small number of independent components mixed with Gaussian noise. These results suggest the ICA model may more accurately represent the data in specific regions of the brain, and that both the activity-dependent sources of blood flow and noise are non-Gaussian.
Group independent component analysis of language fMRI from word generation tasks
NeuroImage, 2008
Language fMRI has been used to study brain regions involved in language processing and has been applied to pre-surgical language mapping. However, in order to provide clinicians with optimal information, the sensitivity and specificity of language fMRI needs to be improved. Type II error of failing to reach statistical significance when the language activations are genuinely present may be particularly relevant to pre-surgical planning, by falsely indicating low surgical risk in areas where no activations are shown. Furthermore, since the execution of language paradigms involves cognitive processes other than language function per se, the conventional general linear model (GLM) method may identify non-language-specific activations. In this study, we assessed an exploratory approach, independent component analysis (ICA), as a potential complementary method to the inferential GLM method in language mapping applications. We specifically investigated whether this approach might reduce type II error as well as generate more language-specific maps. Fourteen right-handed healthy subjects were studied with fMRI during two word generation tasks. A similarity analysis across tasks was proposed to select components of interest. Union analysis was performed on the languagespecific components to increase sensitivity, and conjunction analysis was performed to identify language areas more likely to be essential. Compared with GLM, ICA identified more activated voxels in the putative language areas, and signals from other sources were isolated into different components. Encouraging results from one brain tumor patient are also presented. ICA may be used as a complementary tool to GLM in improving pre-surgical language mapping.
Defining language networks from resting-state fMRI for surgical planning-a feasibility study
Human Brain Mapping, 2013
Presurgical language mapping for patients with lesions close to language areas is critical to neurosurgical decision-making for preservation of language function. As a clinical noninvasive imaging technique, functional MRI (fMRI) is used to identify language areas by measuring bloodoxygen-level dependent (BOLD) signal change while patients perform carefully timed language vs. control tasks. This task-based fMRI critically depends on task performance, excluding many patients who have difficulty performing language tasks due to neurologic deficits. On the basis of recent discovery of resting-state fMRI (rs-fMRI), we propose a "task-free" paradigm acquiring fMRI data when patients simply are at rest. This paradigm is less demanding for patients to perform and easier for technologists to administer. We investigated the feasibility of this approach in right-handed healthy control subjects. First, group independent component analysis (ICA) was applied on the training group (14 subjects) to identify group level language components based on expert rating results. Then, four empirically and structurally defined language network templates were assessed for their ability to identify language components from individuals' ICA output of the testing group (18 subjects) based on spatial similarity analysis. Results suggest that it is feasible to extract language activations from rs-fMRI at the individual subject level, and two empirically defined templates (that focuses on frontal language areas and that incorporates both frontal and temporal language areas) demonstrated the best performance. We propose a semiautomated language component identification procedure and discuss the practical concerns and suggestions for this approach to be used in clinical fMRI language mapping.
Human Brain Mapping, 2013
Atypical functional magnetic resonance imaging (fMRI) language patterns may be identified by visual inspection or by region of interest (ROI)-based laterality indices (LI) but are constrained by a priori assumptions. We compared a data-driven novel application of principal component analysis (PCA) to conventional methods. We studied 122 fMRI data sets from control and localization-related epilepsy patients provided by five children's hospitals. Each subject performed an auditory description decision task. The data sets, acquired with different scanners but similar acquisition parameters, were processed through fMRIB software library to obtain 3D activation maps in standard space. A PCA analysis was applied to generate the decisional space and the data cluster into three distinct activation patterns. The classified activation maps were interpreted by (1) blinded reader rating based on predefined language patterns and (2) by language area ROI-based LI (i.e., fixed threshold vs. bootstrap Published online in Wiley Online Library (wileyonlinelibrary.com).
ICA of Functional MRI Data: An Overview
in Proceedings of the …, 2003
Independent component analysis (ICA) has found a fruitful application in the analysis of functional magnetic resonance imaging (fMRI) data. A principal advantage of this approach is its applicability to cognitive paradigms for which detailed a priori models of brain activity are not ...