3,929 research outputs found
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
Scalable Group Level Probabilistic Sparse Factor Analysis
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 automatic relevance determination (ARD) and subject
specific heteroscedastic spatial noise modeling. For task-based and resting
state fMRI, we show that the sparsity constraint gives rise to components
similar to those obtained by group independent component analysis. The noise
modeling shows that noise is reduced in areas typically associated with
activation by the experimental design. The psFA model identifies sparse
components and the probabilistic setting provides a natural way to handle
parameter uncertainties. The variational Bayesian framework easily extends to
more complex noise models than the presently considered.Comment: 10 pages plus 5 pages appendix, Submitted to ICASSP 1
CanICA: Model-based extraction of reproducible group-level ICA patterns from fMRI time series
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 meaningful patterns without prior
information. However, ICA is not robust to mild data variation and remains a
parameter-sensitive algorithm. The validity of the extracted patterns is hard
to establish, as well as the significance of differences between patterns
extracted from different groups of subjects. We start from a generative model
of the fMRI group data to introduce a probabilistic ICA pattern-extraction
algorithm, called CanICA (Canonical ICA). Thanks to an explicit noise model and
canonical correlation analysis, our method is auto-calibrated and identifies
the group-reproducible data subspace before performing ICA. We compare our
method to state-of-the-art multi-subject fMRI ICA methods and show that the
features extracted are more reproducible
ICA-based sparse feature recovery from fMRI datasets
Spatial Independent Components Analysis (ICA) is increasingly used in the
context of functional Magnetic Resonance Imaging (fMRI) to study cognition and
brain pathologies. Salient features present in some of the extracted
Independent Components (ICs) can be interpreted as brain networks, but the
segmentation of the corresponding regions from ICs is still ill-controlled.
Here we propose a new ICA-based procedure for extraction of sparse features
from fMRI datasets. Specifically, we introduce a new thresholding procedure
that controls the deviation from isotropy in the ICA mixing model. Unlike
current heuristics, our procedure guarantees an exact, possibly conservative,
level of specificity in feature detection. We evaluate the sensitivity and
specificity of the method on synthetic and fMRI data and show that it
outperforms state-of-the-art approaches
Modeling Covariate Effects in Group Independent Component Analysis with Applications to Functional Magnetic Resonance Imaging
Independent component analysis (ICA) is a powerful computational tool for
separating independent source signals from their linear mixtures. ICA has been
widely applied in neuroimaging studies to identify and characterize underlying
brain functional networks. An important goal in such studies is to assess the
effects of subjects' clinical and demographic covariates on the spatial
distributions of the functional networks. Currently, covariate effects are not
incorporated in existing group ICA decomposition methods. Hence, they can only
be evaluated through ad-hoc approaches which may not be accurate in many cases.
In this paper, we propose a hierarchical covariate ICA model that provides a
formal statistical framework for estimating and testing covariate effects in
ICA decomposition. A maximum likelihood method is proposed for estimating the
covariate ICA model. We develop two expectation-maximization (EM) algorithms to
obtain maximum likelihood estimates. The first is an exact EM algorithm, which
has analytically tractable E-step and M-step. Additionally, we propose a
subspace-based approximate EM, which can significantly reduce computational
time while still retain high model-fitting accuracy. Furthermore, to test
covariate effects on the functional networks, we develop a voxel-wise
approximate inference procedure which eliminates the needs of computationally
expensive covariance estimation. The performance of the proposed methods is
evaluated via simulation studies. The application is illustrated through an
fMRI study of Zen meditation.Comment: 36 pages, 5 figure
Tensor Analysis and Fusion of Multimodal Brain Images
Current high-throughput data acquisition technologies probe dynamical systems
with different imaging modalities, generating massive data sets at different
spatial and temporal resolutions posing challenging problems in multimodal data
fusion. A case in point is the attempt to parse out the brain structures and
networks that underpin human cognitive processes by analysis of different
neuroimaging modalities (functional MRI, EEG, NIRS etc.). We emphasize that the
multimodal, multi-scale nature of neuroimaging data is well reflected by a
multi-way (tensor) structure where the underlying processes can be summarized
by a relatively small number of components or "atoms". We introduce
Markov-Penrose diagrams - an integration of Bayesian DAG and tensor network
notation in order to analyze these models. These diagrams not only clarify
matrix and tensor EEG and fMRI time/frequency analysis and inverse problems,
but also help understand multimodal fusion via Multiway Partial Least Squares
and Coupled Matrix-Tensor Factorization. We show here, for the first time, that
Granger causal analysis of brain networks is a tensor regression problem, thus
allowing the atomic decomposition of brain networks. Analysis of EEG and fMRI
recordings shows the potential of the methods and suggests their use in other
scientific domains.Comment: 23 pages, 15 figures, submitted to Proceedings of the IEE
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