Machine learning techniques have gained prominence for the analysis of resting-state functional Magnetic Resonance Imaging (rs-fMRI) data. Here, we present an overview of various unsupervised and supervised machine learning applications to rs-fMRI. We present a methodical taxonomy of machine learning methods in resting…
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48 results for “fMRI analysis”
New model extracts shared brain activity patterns from fMRI data.
problem Challenges in aggregating multi-subject fMRI data due to variability.
method Shared Gaussian Process Factor Analysis (S-GPFA) incorporating temporal information.
result Model reveals ground truth latent structures and replicates experimental performance.
Extracting information from functional magnetic resonance (fMRI) images has been a major area of research for more than two decades. The goal of this work is to present a new method for the analysis of fMRI data sets, that is capable to incorporate a priori available information, via an efficient optimization framework…
Causal discovery improves fMRI analysis, but faces challenges.
problem Challenges in applying causal discovery to fMRI data.
method Identifying and addressing nine challenges in fMRI causal discovery.
result Current methods for fMRI causal discovery need improvement.
Functional Magnetic Resonance Imaging (fMRI) is a powerful non-invasive tool for localizing and analyzing brain activity. This study focuses on one very important aspect of the functional properties of human brain, specifically the estimation of the level of parallelism when performing complex cognitive tasks. Using fM…
Study adapts -TCVAE for fMRI to recover nonlinear brain components.
problem Capturing nonlinear brain dynamics in fMRI data.
method Adapted -TCVAE framework for fMRI data.
result Recovery of meaningful nonlinear spatial components in fMRI data.
Study finds fMRI can predict suicidal ideation, but analysis questions results.
problem Predicting suicidal ideation using fMRI data.
method Naive Bayes classifier trained on fMRI responses to words related to mortality.
result Classification accuracy of 91% for predicting suicidal ideation, but analysis calls into question the accuracy of the findings.
Deep neural networks have been developed drawing inspiration from the brain visual pathway, implementing an end-to-end approach: from image data to video object classes. However building an fMRI decoder with the typical structure of Convolutional Neural Network (CNN), i.e. learning multiple level of representations, se…
Neuroimaging modalities such as functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) provide information about neurological functions in complementary spatiotemporal resolutions; therefore, fusion of these modalities is expected to provide better understanding of brain activity. In this paper, …
Tensor models improve joint EEG and fMRI analysis.
problem Jointly analyzing EEG and fMRI for brain function studies.
method Soft and flexible coupling of tensor decompositions for EEG and fMRI.
result Tensorial methods outperform ICA in multi-modal analysis.
DynDepNet learns dynamic brain graphs from fMRI data for better prediction performance.
problem Static brain graphs from fMRI data lead to poor GNN performance.
method Dynamic Graph Structure Learning for time-varying brain connectivity.
result DynDepNet achieves state-of-the-art sex classification accuracy on real-world fMRI data.
Finding the most effective way to aggregate multi-subject fMRI data is a long-standing and challenging problem. It is of increasing interest in contemporary fMRI studies of human cognition due to the scarcity of data per subject and the variability of brain anatomy and functional response across subjects. Recent work o…
Fine-grained atlases improve fMRI analysis of brain activity.
problem Large fMRI datasets require scalable brain network summaries.
method Trained on millions of fMRI volumes, DiFuMo dictionaries of 64-1024 networks.
result Fine-grained atlases enhance classic fMRI analysis pipelines.
Multi-subject fMRI data analysis is an interesting and challenging problem in human brain decoding studies. The inherent anatomical and functional variability across subjects make it necessary to do both anatomical and functional alignment before classification analysis. Besides, when it comes to big data, time complex…
A novel method automates quality control of fMRI scans, improving accuracy and generalizability.
problem Lack of automated QC for fMRI scans limits clinical neuroscience research.
method Train machine learning classifiers using runtime log features to predict scan quality.
result Classifiers trained on FLAG-QC features outperform previous methods (AUC=0.79 vs AUC=0.56).
In order to decode the human brain, Multivariate Pattern (MVP) classification generates cognitive models by using functional Magnetic Resonance Imaging (fMRI) datasets. As a standard pipeline in the MVP analysis, brain patterns in multi-subject fMRI dataset must be mapped to a shared space and then a classification mod…
SHA improves fMRI alignment for cognitive state discovery.
problem Optimal functional alignment in MVP analysis for multi-subject fMRI data.
method Supervised Hyperalignment (SHA) method that maximizes correlation within same categories and minimizes between distinct categories.
result SHA achieves up to 19% better performance for multi-class problems.
ST-GCN improves rs-fMRI prediction accuracy by modeling spatio-temporal graph connectivity.
problem Existing rs-fMRI methods neglect functional connectivity or temporal dynamics.
method Spatio-temporal graph convolutional network (ST-GCN) trained on BOLD time series.
result ST-GCN predicts gender and age more accurately than common methods.
Variation Autoencoder (VAE) has become a powerful tool in modeling the non-linear generative process of data from a low-dimensional latent space. Recently, several studies have proposed to use VAE for unsupervised clustering by using mixture models to capture the multi-modal structure of latent representations. This st…
Develops GIN for fMRI sex classification, explaining results.
problem Difficulty in explaining GNN classification results in neuroscientific terms.
method Develops Graph Isomorphism Network (GIN) for fMRI data, leveraging CNN saliency maps.
result GIN enables visualization of brain regions important for sex classification.
A novel topological method analyzes fMRI data over time.
problem Analyzing time-varying fMRI data due to noise and person-to-person variation.
method Encoding each time point as a persistence diagram of topological features.
result Time-varying persistence diagrams can cluster participants and study brain state trajectories.
Framework identifies brain connectivity alterations for MDD patients using limited rs-fMRI data.
problem Difficult to analyze brain connectivity alterations from limited rs-fMRI data.
method Proposed a multitask Gaussian Bayesian network (MTGBN) framework to learn individual disease-induced alterations.
result Framework efficiently learns Bayesian network structures from limited data, showing improved performance.
The growing use of neuroimaging technologies generates a massive amount of biomedical data that exhibit high dimensionality. Tensor-based analysis of brain imaging data has been proved quite effective in exploiting their multiway nature. The advantages of tensorial methods over matrix-based approaches have also been de…
A new ICA method adds L1-regularization for better interpretability of fMRI data.
problem Improving interpretability of ICA features in high-dimensional fMRI data.
method L1-regularization added to ICA cost function, solved by DCA.
result Validated on synthetic and real fMRI data, improving feature interpretability.
Novel algorithm for private analysis of fMRI data.
problem Privacy concerns in collaborative neuroimaging data analysis.
method Differentially private decentralized ICA algorithm using correlated noise.
result Algorithm outperforms existing methods on synthetic and real neuroimaging datasets.
Background: Functional magnetic resonance imaging (fMRI) provides non-invasive measures of neuronal activity using an endogenous Blood Oxygenation-Level Dependent (BOLD) contrast. This article introduces a nonlinear dimensionality reduction (Locally Linear Embedding) to extract informative measures of the underlying ne…
Reconstructing observed images from fMRI brain recordings is challenging. Unfortunately, acquiring sufficient "labeled" pairs of {Image, fMRI} (i.e., images with their corresponding fMRI responses) to span the huge space of natural images is prohibitive for many reasons. We present a novel approach which, in addition t…
A Searchlight Factor Model Approach for Locating Shared Information in Multi-Subject fMRI Analysisstat.ML
There is a growing interest in joint multi-subject fMRI analysis. The challenge of such analysis comes from inherent anatomical and functional variability across subjects. One approach to resolving this is a shared response factor model. This assumes a shared and time synchronized stimulus across subjects. Such a model…
Understanding human fetal neurodevelopment is of great clinical importance as abnormal development is linked to adverse neuropsychiatric outcomes after birth. Recent advances in functional Magnetic Resonance Imaging (fMRI) have provided new insight into development of the human brain before birth, but these studies hav…
The application of deep learning (DL) models to neuroimaging data poses several challenges, due to the high dimensionality, low sample size and complex temporo-spatial dependency structure of these datasets. Even further, DL models act as as black-box models, impeding insight into the association of cognitive state and…
A simplified model for brain activity measurement.
problem Estimating the BOLD response in fMRI data.
method Proposes a lightweight model for HRF with fewer parameters.
result Reduces optimization complexity and facilitates applications.
It becomes increasingly popular to perform mediation analysis for complex data from sophisticated experimental studies. In this paper, we present Granger Mediation Analysis (GMA), a new framework for causal mediation analysis of multiple time series. This framework is motivated by a functional magnetic resonance imagin…
BrainCast predicts whole-brain fMRI time series from short scans.
problem Short scans reduce fMRI data quality and statistical power.
method Spatio-temporal forecasting framework for fMRI time series.
result BrainCast improves fMRI time series quality and prediction.
Many data-driven approaches exist to extract neural representations of functional magnetic resonance imaging (fMRI) data, but most of them lack a proper probabilistic formulation. We propose a group level scalable probabilistic sparse factor analysis (psFA) allowing spatially sparse maps, component pruning using automa…
Functional Magnetic Resonance Imaging (fMRI) relies on multi-step data processing pipelines to accurately determine brain activity; among them, the crucial step of spatial smoothing. These pipelines are commonly suboptimal, given the local optimisation strategy they use, treating each step in isolation. With the advent…
Gradient-based Representational Similarity Analysis with Searchlight for Analyzing fMRI Dataq-bio.NC
Representational Similarity Analysis (RSA) aims to explore similarities between neural activities of different stimuli. Classical RSA techniques employ the inverse of the covariance matrix to explore a linear model between the neural activities and task events. However, calculating the inverse of a large-scale covarian…
We propose a novel two-phase approach to functional network estimation of multi-subject functional Magnetic Resonance Imaging (fMRI) data, which applies model-based image segmentation to determine a group-representative connectivity map. In our approach, we first improve clustering-based Independent Component Analysis …
Learning a similarity metric has gained much attention recently, where the goal is to learn a function that maps input patterns to a target space while preserving the semantic distance in the input space. While most related work focused on images, we focus instead on learning a similarity metric for neuroimages, such a…
Aggregating multi-subject functional magnetic resonance imaging (fMRI) data is indispensable for generating valid and general inferences from patterns distributed across human brains. The disparities in anatomical structures and functional topographies of human brains warrant aligning fMRI data across subjects. However…
Paper introduces a framework for diagnosing Alzheimer's disease using higher-order topological features from fMRI.
problem Diagnosing Alzheimer's disease using brain network topology.
method Persistent homology to extract higher-order features (cycles, cavities) from fMRI data.
result Framework significantly outperforms existing methods in AD classification.
In this paper, the task-related fMRI problem is treated in its matrix factorization formulation, focused on the Dictionary Learning (DL) approach. The new method allows the incorporation of a priori knowledge associated both with the experimental design as well as with available brain Atlases. Moreover, the proposed me…
New methods improve brain data analysis from fMRI datasets.
problem Simplified brain models from correlational values are insufficient.
method Deep learning and geometric deep learning techniques.
result Improved predictive spatio-temporal brain data representation.
A major tenet in theoretical neuroscience is that cognitive and behavioral processes are ultimately implemented in terms of the neural system dynamics. Accordingly, a major aim for the analysis of neurophysiological measurements should lie in the identification of the computational dynamics underlying task processing. …
This study shows how EEG can be used to generate fMRI data.
problem Mapping fMRI from EEG signals.
method Deep learning approaches (Autoencoders, GANs, Pairwise Learning).
result Feasibility of EEG to fMRI brain image mappings.
Survey of deep learning methods for fMRI natural image reconstruction.
problem Reconstructing natural images from fMRI brain activity.
method Survey of deep learning approaches, including architectural design, datasets, and evaluation metrics.
result Performance evaluation across standardized metrics.
Multivariate Pattern (MVP) classification can map different cognitive states to the brain tasks. One of the main challenges in MVP analysis is validating the generated results across subjects. However, analyzing multi-subject fMRI data requires accurate functional alignments between neuronal activities of different sub…
Deep Hyperalignmentq-bio.NC
This paper proposes Deep Hyperalignment (DHA) as a regularized, deep extension, scalable Hyperalignment (HA) method, which is well-suited for applying functional alignment to fMRI datasets with nonlinearity, high-dimensionality (broad ROI), and a large number of subjects. Unlink previous methods, DHA is not limited by …
Paper presents a method to diagnose schizophrenia using fMRI dynamics from healthy controls.
problem Early diagnosis of mental disorders like schizophrenia using fMRI.
method Self-supervised pre-training on fMRI dynamics of healthy controls for transfer learning.
result Effective classification of schizophrenia using fMRI dynamics with small datasets.