370 research outputs found
Compressed Online Dictionary Learning for Fast fMRI Decomposition
We present a method for fast resting-state fMRI spatial decomposi-tions of
very large datasets, based on the reduction of the temporal dimension before
applying dictionary learning on concatenated individual records from groups of
subjects. Introducing a measure of correspondence between spatial
decompositions of rest fMRI, we demonstrates that time-reduced dictionary
learning produces result as reliable as non-reduced decompositions. We also
show that this reduction significantly improves computational scalability
Social-sparsity brain decoders: faster spatial sparsity
Spatially-sparse predictors are good models for brain decoding: they give
accurate predictions and their weight maps are interpretable as they focus on a
small number of regions. However, the state of the art, based on total
variation or graph-net, is computationally costly. Here we introduce sparsity
in the local neighborhood of each voxel with social-sparsity, a structured
shrinkage operator. We find that, on brain imaging classification problems,
social-sparsity performs almost as well as total-variation models and better
than graph-net, for a fraction of the computational cost. It also very clearly
outlines predictive regions. We give details of the model and the algorithm.Comment: in Pattern Recognition in NeuroImaging, Jun 2016, Trento, Italy. 201
Mapping cognitive ontologies to and from the brain
Imaging neuroscience links brain activation maps to behavior and cognition
via correlational studies. Due to the nature of the individual experiments,
based on eliciting neural response from a small number of stimuli, this link is
incomplete, and unidirectional from the causal point of view. To come to
conclusions on the function implied by the activation of brain regions, it is
necessary to combine a wide exploration of the various brain functions and some
inversion of the statistical inference. Here we introduce a methodology for
accumulating knowledge towards a bidirectional link between observed brain
activity and the corresponding function. We rely on a large corpus of imaging
studies and a predictive engine. Technically, the challenges are to find
commonality between the studies without denaturing the richness of the corpus.
The key elements that we contribute are labeling the tasks performed with a
cognitive ontology, and modeling the long tail of rare paradigms in the corpus.
To our knowledge, our approach is the first demonstration of predicting the
cognitive content of completely new brain images. To that end, we propose a
method that predicts the experimental paradigms across different studies.Comment: NIPS (Neural Information Processing Systems), United States (2013
On spatial selectivity and prediction across conditions with fMRI
Researchers in functional neuroimaging mostly use activation coordinates to
formulate their hypotheses. Instead, we propose to use the full statistical
images to define regions of interest (ROIs). This paper presents two machine
learning approaches, transfer learning and selection transfer, that are
compared upon their ability to identify the common patterns between brain
activation maps related to two functional tasks. We provide some preliminary
quantification of these similarities, and show that selection transfer makes it
possible to set a spatial scale yielding ROIs that are more specific to the
context of interest than with transfer learning. In particular, selection
transfer outlines well known regions such as the Visual Word Form Area when
discriminating between different visual tasks.Comment: PRNI 2012 : 2nd International Workshop on Pattern Recognition in
NeuroImaging, London : United Kingdom (2012
HRF estimation improves sensitivity of fMRI encoding and decoding models
Extracting activation patterns from functional Magnetic Resonance Images
(fMRI) datasets remains challenging in rapid-event designs due to the inherent
delay of blood oxygen level-dependent (BOLD) signal. The general linear model
(GLM) allows to estimate the activation from a design matrix and a fixed
hemodynamic response function (HRF). However, the HRF is known to vary
substantially between subjects and brain regions. In this paper, we propose a
model for jointly estimating the hemodynamic response function (HRF) and the
activation patterns via a low-rank representation of task effects.This model is
based on the linearity assumption behind the GLM and can be computed using
standard gradient-based solvers. We use the activation patterns computed by our
model as input data for encoding and decoding studies and report performance
improvement in both settings.Comment: 3nd International Workshop on Pattern Recognition in NeuroImaging
(2013
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
Brain covariance selection: better individual functional connectivity models using population prior
Spontaneous brain activity, as observed in functional neuroimaging, has been
shown to display reproducible structure that expresses brain architecture and
carries markers of brain pathologies. An important view of modern neuroscience
is that such large-scale structure of coherent activity reflects modularity
properties of brain connectivity graphs. However, to date, there has been no
demonstration that the limited and noisy data available in spontaneous activity
observations could be used to learn full-brain probabilistic models that
generalize to new data. Learning such models entails two main challenges: i)
modeling full brain connectivity is a difficult estimation problem that faces
the curse of dimensionality and ii) variability between subjects, coupled with
the variability of functional signals between experimental runs, makes the use
of multiple datasets challenging. We describe subject-level brain functional
connectivity structure as a multivariate Gaussian process and introduce a new
strategy to estimate it from group data, by imposing a common structure on the
graphical model in the population. We show that individual models learned from
functional Magnetic Resonance Imaging (fMRI) data using this population prior
generalize better to unseen data than models based on alternative
regularization schemes. To our knowledge, this is the first report of a
cross-validated model of spontaneous brain activity. Finally, we use the
estimated graphical model to explore the large-scale characteristics of
functional architecture and show for the first time that known cognitive
networks appear as the integrated communities of functional connectivity graph.Comment: in Advances in Neural Information Processing Systems, Vancouver :
Canada (2010
Second order scattering descriptors predict fMRI activity due to visual textures
Second layer scattering descriptors are known to provide good classification
performance on natural quasi-stationary processes such as visual textures due
to their sensitivity to higher order moments and continuity with respect to
small deformations. In a functional Magnetic Resonance Imaging (fMRI)
experiment we present visual textures to subjects and evaluate the predictive
power of these descriptors with respect to the predictive power of simple
contour energy - the first scattering layer. We are able to conclude not only
that invariant second layer scattering coefficients better encode voxel
activity, but also that well predicted voxels need not necessarily lie in known
retinotopic regions.Comment: 3nd International Workshop on Pattern Recognition in NeuroImaging
(2013
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