KEYWORDS: Visualization, Functional magnetic resonance imaging, Brain, Stochastic processes, Principal component analysis, Signal to noise ratio, Neuroimaging, Hemodynamics, Magnetic resonance imaging, Interference (communication)
Purpose: Currently, functional magnetic resonance imaging (fMRI) is the most commonly used technique for obtaining dynamic information about the brain. However, because of the complexity of the data, it is often difficult to directly visualize the temporal aspect of the fMRI data.
Approach: We outline a t-distributed stochastic neighbor embedding (t-SNE)-based postprocessing technique that can be used for visualization of temporal information from a 4D fMRI data. Apart from visualization, we also show its utility in detection of major changes in the brain meta-states during the scan duration.
Results: The t-SNE approach is able to detect brain-state changes from task to rest and vice versa for single- and multitask fMRI data. A temporal visualization can also be obtained for task and resting state fMRI data for assessing the temporal dynamics during the scan duration. Additionally, hemodynamic delay can be quantified by comparison of the detected brain-state changes with the experiment paradigm for task fMRI data.
Conclusion: The t-SNE visualization can visualize help identify major brain-state changes from fMRI data. Such visualization can provide information about the degree of involvement and attentiveness of the subject during the scan and can be potentially utilized as a quality control for subject’s performance during the scan.
Purpose: Through the last three decades, functional magnetic resonance imaging (fMRI) has provided immense quantities of information about the dynamics of the brain, functional brain mapping, and resting-state brain networks. Despite providing such rich functional information, fMRI is still not a commonly used clinical technique due to inaccuracy involved in analysis of extremely noisy data. However, ongoing developments in deep learning techniques suggest potential improvements and better performance in many different domains. Our main purpose is to utilize the potentials of deep learning techniques for fMRI data for clinical use.
Approach: We present one such synergy of fMRI and deep learning, where we apply a simplified yet accurate method using a modified 3D convolutional neural networks (CNN) to resting-state fMRI data for feature extraction and classification of Alzheimer’s disease (AD). The CNN is designed in such a way that it uses the fMRI data with much less preprocessing, preserving both spatial and temporal information.
Results: Once trained, the network is successfully able to classify between fMRI data from healthy controls and AD subjects, including subjects in the mild cognitive impairment (MCI) stage. We have also extracted spatiotemporal features useful for classification.
Conclusion: This CNN can detect and differentiate between the earlier and later stages of MCI and AD and hence, it may have potential clinical applications in both early detection and better diagnosis of Alzheimer’s disease.
Functional magnetic resonance imaging has a potential to provide insight into early detectors or biomarkers for various neurological disorders. With the advent of recent developments in deep learning, it may be possible to extract detailed information from neuroimaging data that is difficult to acquire using traditional techniques. Here we propose one such deep learning approach that makes use of a 3D Convolutional Neural Network to predict the onset of Alzheimer’s disease even in a single subject based on resting state fMRI data. This approach extracts both spatial and temporal features from the 4D volume and eliminates the traditional complicated steps of feature extraction. In our experiments, a relatively simple deep learning architecture yields high performance in Alzheimer’s disease classification. This illustrates the possibility of using volumetric feature extractors and classifiers as a tool to obtain biomarkers for neurological disorders and another step towards use of clinical fMRI.
KEYWORDS: Functional magnetic resonance imaging, Principal component analysis, Brain, Data analysis, Magnetic resonance imaging, Signal detection, Hemodynamics, Magnetism
Temporal signal drift is one of the significant artifacts in functional Magnetic Resonance Imaging (fMRI) data that is not given as much attention as motion or physiological artifacts. However, signal drift if not accounted for, can introduce spurious correlation between different regions in resting state fMRI data. Hence detection and removal of signal drift is an important preprocessing step in fMRI data analysis. Here we propose an automated data driven approach that makes use of Principal Component Analysis (PCA) to eliminate not only low frequency signal drift but also spontaneous high frequency global signal fluctuations. This approach is also able to identify the most dominant component for each voxel separately. For task fMRI, this can help us identify regions that respond in a time locked manner to the experiment paradigm. Such regions can be thought of as activation regions. The dominant principal components corresponding to such regions can also be used to investigate intra-region Hemodynamic Response (HR) variability within subjects and across subjects.
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