4,095 research outputs found
PEAR: PEriodic And fixed Rank separation for fast fMRI
In functional MRI (fMRI), faster acquisition via undersampling of data can
improve the spatial-temporal resolution trade-off and increase statistical
robustness through increased degrees-of-freedom. High quality reconstruction of
fMRI data from undersampled measurements requires proper modeling of the data.
We present an fMRI reconstruction approach based on modeling the fMRI signal as
a sum of periodic and fixed rank components, for improved reconstruction from
undersampled measurements. We decompose the fMRI signal into a component which
a has fixed rank and a component consisting of a sum of periodic signals which
is sparse in the temporal Fourier domain. Data reconstruction is performed by
solving a constrained problem that enforces a fixed, moderate rank on one of
the components, and a limited number of temporal frequencies on the other. Our
approach is coined PEAR - PEriodic And fixed Rank separation for fast fMRI.
Experimental results include purely synthetic simulation, a simulation with
real timecourses and retrospective undersampling of a real fMRI dataset.
Evaluation was performed both quantitatively and visually versus ground truth,
comparing PEAR to two additional recent methods for fMRI reconstruction from
undersampled measurements. Results demonstrate PEAR's improvement in estimating
the timecourses and activation maps versus the methods compared against at
acceleration ratios of R=8,16 (for simulated data) and R=6.66,10 (for real
data). PEAR results in reconstruction with higher fidelity than when using a
fixed-rank based model or a conventional Low-rank+Sparse algorithm. We have
shown that splitting the functional information between the components leads to
better modeling of fMRI, over state-of-the-art methods
Markov models for fMRI correlation structure: is brain functional connectivity small world, or decomposable into networks?
Correlations in the signal observed via functional Magnetic Resonance Imaging
(fMRI), are expected to reveal the interactions in the underlying neural
populations through hemodynamic response. In particular, they highlight
distributed set of mutually correlated regions that correspond to brain
networks related to different cognitive functions. Yet graph-theoretical
studies of neural connections give a different picture: that of a highly
integrated system with small-world properties: local clustering but with short
pathways across the complete structure. We examine the conditional independence
properties of the fMRI signal, i.e. its Markov structure, to find realistic
assumptions on the connectivity structure that are required to explain the
observed functional connectivity. In particular we seek a decomposition of the
Markov structure into segregated functional networks using decomposable graphs:
a set of strongly-connected and partially overlapping cliques. We introduce a
new method to efficiently extract such cliques on a large, strongly-connected
graph. We compare methods learning different graph structures from functional
connectivity by testing the goodness of fit of the model they learn on new
data. We find that summarizing the structure as strongly-connected networks can
give a good description only for very large and overlapping networks. These
results highlight that Markov models are good tools to identify the structure
of brain connectivity from fMRI signals, but for this purpose they must reflect
the small-world properties of the underlying neural systems
A blind deconvolution approach to recover effective connectivity brain networks from resting state fMRI data
A great improvement to the insight on brain function that we can get from
fMRI data can come from effective connectivity analysis, in which the flow of
information between even remote brain regions is inferred by the parameters of
a predictive dynamical model. As opposed to biologically inspired models, some
techniques as Granger causality (GC) are purely data-driven and rely on
statistical prediction and temporal precedence. While powerful and widely
applicable, this approach could suffer from two main limitations when applied
to BOLD fMRI data: confounding effect of hemodynamic response function (HRF)
and conditioning to a large number of variables in presence of short time
series. For task-related fMRI, neural population dynamics can be captured by
modeling signal dynamics with explicit exogenous inputs; for resting-state fMRI
on the other hand, the absence of explicit inputs makes this task more
difficult, unless relying on some specific prior physiological hypothesis. In
order to overcome these issues and to allow a more general approach, here we
present a simple and novel blind-deconvolution technique for BOLD-fMRI signal.
Coming to the second limitation, a fully multivariate conditioning with short
and noisy data leads to computational problems due to overfitting. Furthermore,
conceptual issues arise in presence of redundancy. We thus apply partial
conditioning to a limited subset of variables in the framework of information
theory, as recently proposed. Mixing these two improvements we compare the
differences between BOLD and deconvolved BOLD level effective networks and draw
some conclusions
Machine Learning for Neuroimaging with Scikit-Learn
Statistical machine learning methods are increasingly used for neuroimaging
data analysis. Their main virtue is their ability to model high-dimensional
datasets, e.g. multivariate analysis of activation images or resting-state time
series. Supervised learning is typically used in decoding or encoding settings
to relate brain images to behavioral or clinical observations, while
unsupervised learning can uncover hidden structures in sets of images (e.g.
resting state functional MRI) or find sub-populations in large cohorts. By
considering different functional neuroimaging applications, we illustrate how
scikit-learn, a Python machine learning library, can be used to perform some
key analysis steps. Scikit-learn contains a very large set of statistical
learning algorithms, both supervised and unsupervised, and its application to
neuroimaging data provides a versatile tool to study the brain.Comment: Frontiers in neuroscience, Frontiers Research Foundation, 2013, pp.1
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