4,926 research outputs found
Hierarchical Bayesian sparse image reconstruction with application to MRFM
This paper presents a hierarchical Bayesian model to reconstruct sparse
images when the observations are obtained from linear transformations and
corrupted by an additive white Gaussian noise. Our hierarchical Bayes model is
well suited to such naturally sparse image applications as it seamlessly
accounts for properties such as sparsity and positivity of the image via
appropriate Bayes priors. We propose a prior that is based on a weighted
mixture of a positive exponential distribution and a mass at zero. The prior
has hyperparameters that are tuned automatically by marginalization over the
hierarchical Bayesian model. To overcome the complexity of the posterior
distribution, a Gibbs sampling strategy is proposed. The Gibbs samples can be
used to estimate the image to be recovered, e.g. by maximizing the estimated
posterior distribution. In our fully Bayesian approach the posteriors of all
the parameters are available. Thus our algorithm provides more information than
other previously proposed sparse reconstruction methods that only give a point
estimate. The performance of our hierarchical Bayesian sparse reconstruction
method is illustrated on synthetic and real data collected from a tobacco virus
sample using a prototype MRFM instrument.Comment: v2: final version; IEEE Trans. Image Processing, 200
Fractal analysis of resting state functional connectivity of the brain
A variety of resting state neuroimaging data tend to exhibit fractal behavior
where its power spectrum follows power-law scaling. Resting state functional
connectivity is significantly influenced by fractal behavior which may not
directly originate from neuronal population activities of the brain. To
describe the fractal behavior, we adopted the fractionally integrated process
(FIP) model instead of the fractional Gaussian noise (FGN) since the FIP model
covers more general aspects of fractality than the FGN model. We also introduce
a novel concept called the nonfractal connectivity which is defined as the
correlation of short memory independent of fractal behavior, and compared it
with the fractal connectivity which is an asymptotic wavelet correlation. We
propose several wavelet-based estimators of fractal connectivity and nonfractal
connectivity for a multivariate fractionally integrated noise (mFIN). The
performance of these estimators was evaluated through simulation studies and
the analyses of resting state functional MRI data of the rat brain.Comment: The 2012 International Joint Conference on Neural Network
Variational semi-blind sparse deconvolution with orthogonal kernel bases and its application to MRFM
We present a variational Bayesian method of joint image reconstruction and point spread function (PSF) estimation when the PSF of the imaging device is only partially known. To solve this semi-blind deconvolution problem, prior distributions are specified for the PSF and the 3D image. Joint image reconstruction and PSF estimation is then performed within a Bayesian framework, using a variational algorithm to estimate the posterior distribution. The image prior distribution imposes an explicit atomic measure that corresponds to image sparsity. Importantly, the proposed Bayesian deconvolution algorithm does not require hand tuning. Simulation results clearly demonstrate that the semi-blind deconvolution algorithm compares favorably with previous Markov chain Monte Carlo (MCMC) version of myopic sparse reconstruction. It significantly outperforms mismatched non-blind algorithms that rely on the assumption of the perfect knowledge of the PSF. The algorithm is illustrated on real data from magnetic resonance force microscopy (MRFM)
Variational semi-blind sparse deconvolution with orthogonal kernel bases and its application to MRFM
We present a variational Bayesian method of joint image reconstruction and point spread function (PSF) estimation when the PSF of the imaging device is only partially known. To solve this semi-blind deconvolution problem, prior distributions are specified for the PSF and the 3D image. Joint image reconstruction and PSF estimation is then performed within a Bayesian framework, using a variational algorithm to estimate the posterior distribution. The image prior distribution imposes an explicit atomic measure that corresponds to image sparsity. Importantly, the proposed Bayesian deconvolution algorithm does not require hand tuning. Simulation results clearly demonstrate that the semi-blind deconvolution algorithm compares favorably with previous Markov chain Monte Carlo (MCMC) version of myopic sparse reconstruction. It significantly outperforms mismatched non-blind algorithms that rely on the assumption of the perfect knowledge of the PSF. The algorithm is illustrated on real data from magnetic resonance force microscopy (MRFM)
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
A Multiscale Approach for Statistical Characterization of Functional Images
Increasingly, scientific studies yield functional image data, in which the observed data consist of sets of curves recorded on the pixels of the image. Examples include temporal brain response intensities measured by fMRI and NMR frequency spectra measured at each pixel. This article presents a new methodology for improving the characterization of pixels in functional imaging, formulated as a spatial curve clustering problem. Our method operates on curves as a unit. It is nonparametric and involves multiple stages: (i) wavelet thresholding, aggregation, and Neyman truncation to effectively reduce dimensionality; (ii) clustering based on an extended EM algorithm; and (iii) multiscale penalized dyadic partitioning to create a spatial segmentation. We motivate the different stages with theoretical considerations and arguments, and illustrate the overall procedure on simulated and real datasets. Our method appears to offer substantial improvements over monoscale pixel-wise methods. An Appendix which gives some theoretical justifications of the methodology, computer code, documentation and dataset are available in the online supplements
Sparse image reconstruction for molecular imaging
The application that motivates this paper is molecular imaging at the atomic
level. When discretized at sub-atomic distances, the volume is inherently
sparse. Noiseless measurements from an imaging technology can be modeled by
convolution of the image with the system point spread function (psf). Such is
the case with magnetic resonance force microscopy (MRFM), an emerging
technology where imaging of an individual tobacco mosaic virus was recently
demonstrated with nanometer resolution. We also consider additive white
Gaussian noise (AWGN) in the measurements. Many prior works of sparse
estimators have focused on the case when H has low coherence; however, the
system matrix H in our application is the convolution matrix for the system
psf. A typical convolution matrix has high coherence. The paper therefore does
not assume a low coherence H. A discrete-continuous form of the Laplacian and
atom at zero (LAZE) p.d.f. used by Johnstone and Silverman is formulated, and
two sparse estimators derived by maximizing the joint p.d.f. of the observation
and image conditioned on the hyperparameters. A thresholding rule that
generalizes the hard and soft thresholding rule appears in the course of the
derivation. This so-called hybrid thresholding rule, when used in the iterative
thresholding framework, gives rise to the hybrid estimator, a generalization of
the lasso. Unbiased estimates of the hyperparameters for the lasso and hybrid
estimator are obtained via Stein's unbiased risk estimate (SURE). A numerical
study with a Gaussian psf and two sparse images shows that the hybrid estimator
outperforms the lasso.Comment: 12 pages, 8 figure
Automatic, fast and robust characterization of noise distributions for diffusion MRI
Knowledge of the noise distribution in magnitude diffusion MRI images is the
centerpiece to quantify uncertainties arising from the acquisition process. The
use of parallel imaging methods, the number of receiver coils and imaging
filters applied by the scanner, amongst other factors, dictate the resulting
signal distribution. Accurate estimation beyond textbook Rician or noncentral
chi distributions often requires information about the acquisition process
(e.g. coils sensitivity maps or reconstruction coefficients), which is not
usually available. We introduce a new method where a change of variable
naturally gives rise to a particular form of the gamma distribution for
background signals. The first moments and maximum likelihood estimators of this
gamma distribution explicitly depend on the number of coils, making it possible
to estimate all unknown parameters using only the magnitude data. A rejection
step is used to make the method automatic and robust to artifacts. Experiments
on synthetic datasets show that the proposed method can reliably estimate both
the degrees of freedom and the standard deviation. The worst case errors range
from below 2% (spatially uniform noise) to approximately 10% (spatially
variable noise). Repeated acquisitions of in vivo datasets show that the
estimated parameters are stable and have lower variances than compared methods.Comment: v2: added publisher DOI statement, fixed text typo in appendix A
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