3,769 research outputs found
Meta-analysis of functional neuroimaging data using Bayesian nonparametric binary regression
In this work we perform a meta-analysis of neuroimaging data, consisting of
locations of peak activations identified in 162 separate studies on emotion.
Neuroimaging meta-analyses are typically performed using kernel-based methods.
However, these methods require the width of the kernel to be set a priori and
to be constant across the brain. To address these issues, we propose a fully
Bayesian nonparametric binary regression method to perform neuroimaging
meta-analyses. In our method, each location (or voxel) has a probability of
being a peak activation, and the corresponding probability function is based on
a spatially adaptive Gaussian Markov random field (GMRF). We also include
parameters in the model to robustify the procedure against miscoding of the
voxel response. Posterior inference is implemented using efficient MCMC
algorithms extended from those introduced in Holmes and Held [Bayesian Anal. 1
(2006) 145--168]. Our method allows the probability function to be locally
adaptive with respect to the covariates, that is, to be smooth in one region of
the covariate space and wiggly or even discontinuous in another. Posterior
miscoding probabilities for each of the identified voxels can also be obtained,
identifying voxels that may have been falsely classified as being activated.
Simulation studies and application to the emotion neuroimaging data indicate
that our method is superior to standard kernel-based methods.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS523 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Semiparametric Bayesian models for human brain mapping
Functional magnetic resonance imaging (fMRI) has led to enormous progress in human brain mapping. Adequate analysis of the massive spatiotemporal data sets generated by this imaging technique, combining parametric and non-parametric components, imposes challenging problems in statistical modelling. Complex hierarchical Bayesian models in combination with computer-intensive Markov chain Monte Carlo inference are promising tools.The purpose of this paper is twofold. First, it provides a review of general semiparametric Bayesian models for the analysis of fMRI data. Most approaches focus on important but separate temporal or spatial aspects of the overall problem, or they proceed by stepwise procedures. Therefore, as a second aim, we suggest a complete spatiotemporal model for analysing fMRI data within a unified semiparametric Bayesian framework. An application to data from a visual stimulation experiment illustrates our approach and demonstrates its computational feasibility
Multiscale adaptive smoothing models for the hemodynamic response function in fMRI
In the event-related functional magnetic resonance imaging (fMRI) data
analysis, there is an extensive interest in accurately and robustly estimating
the hemodynamic response function (HRF) and its associated statistics (e.g.,
the magnitude and duration of the activation). Most methods to date are
developed in the time domain and they have utilized almost exclusively the
temporal information of fMRI data without accounting for the spatial
information. The aim of this paper is to develop a multiscale adaptive
smoothing model (MASM) in the frequency domain by integrating the spatial and
frequency information to adaptively and accurately estimate HRFs pertaining to
each stimulus sequence across all voxels in a three-dimensional (3D) volume. We
use two sets of simulation studies and a real data set to examine the finite
sample performance of MASM in estimating HRFs. Our real and simulated data
analyses confirm that MASM outperforms several other state-of-the-art methods,
such as the smooth finite impulse response (sFIR) model.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS609 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
The empirical replicability of task-based fMRI as a function of sample size
Replicating results (i.e. obtaining consistent results using a new independent dataset) is an essential part of good science. As replicability has consequences for theories derived from empirical studies, it is of utmost importance to better understand the underlying mechanisms influencing it. A popular tool for non-invasive neuroimaging studies is functional magnetic resonance imaging (fMRI). While the effect of underpowered studies is well documented, the empirical assessment of the interplay between sample size and replicability of results for task-based fMRI studies remains limited. In this work, we extend existing work on this assessment in two ways. Firstly, we use a large database of 1400 subjects performing four types of tasks from the IMAGEN project to subsample a series of independent samples of increasing size. Secondly, replicability is evaluated using a multi-dimensional framework consisting of 3 different measures: (un)conditional test-retest reliability, coherence and stability. We demonstrate not only a positive effect of sample size, but also a trade-off between spatial resolution and replicability. When replicability is assessed voxelwise or when observing small areas of activation, a larger sample size than typically used in fMRI is required to replicate results. On the other hand, when focussing on clusters of voxels, we observe a higher replicability. In addition, we observe variability in the size of clusters of activation between experimental paradigms or contrasts of parameter estimates within these
A simple and objective method for reproducible resting state network (RSN) detection in fMRI
Spatial Independent Component Analysis (ICA) decomposes the time by space
functional MRI (fMRI) matrix into a set of 1-D basis time courses and their
associated 3-D spatial maps that are optimized for mutual independence. When
applied to resting state fMRI (rsfMRI), ICA produces several spatial
independent components (ICs) that seem to have biological relevance - the
so-called resting state networks (RSNs). The ICA problem is well posed when the
true data generating process follows a linear mixture of ICs model in terms of
the identifiability of the mixing matrix. However, the contrast function used
for promoting mutual independence in ICA is dependent on the finite amount of
observed data and is potentially non-convex with multiple local minima. Hence,
each run of ICA could produce potentially different IC estimates even for the
same data. One technique to deal with this run-to-run variability of ICA was
proposed by Yang et al. (2008) in their algorithm RAICAR which allows for the
selection of only those ICs that have a high run-to-run reproducibility. We
propose an enhancement to the original RAICAR algorithm that enables us to
assign reproducibility p-values to each IC and allows for an objective
assessment of both within subject and across subjects reproducibility. We call
the resulting algorithm RAICAR-N (N stands for null hypothesis test), and we
have applied it to publicly available human rsfMRI data (http://www.nitrc.org).
Our reproducibility analyses indicated that many of the published RSNs in
rsfMRI literature are highly reproducible. However, we found several other RSNs
that are highly reproducible but not frequently listed in the literature.Comment: 54 pages, 13 figure
Physiological Gaussian Process Priors for the Hemodynamics in fMRI Analysis
Background: Inference from fMRI data faces the challenge that the hemodynamic
system that relates neural activity to the observed BOLD fMRI signal is
unknown.
New Method: We propose a new Bayesian model for task fMRI data with the
following features: (i) joint estimation of brain activity and the underlying
hemodynamics, (ii) the hemodynamics is modeled nonparametrically with a
Gaussian process (GP) prior guided by physiological information and (iii) the
predicted BOLD is not necessarily generated by a linear time-invariant (LTI)
system. We place a GP prior directly on the predicted BOLD response, rather
than on the hemodynamic response function as in previous literature. This
allows us to incorporate physiological information via the GP prior mean in a
flexible way, and simultaneously gives us the nonparametric flexibility of the
GP.
Results: Results on simulated data show that the proposed model is able to
discriminate between active and non-active voxels also when the GP prior
deviates from the true hemodynamics. Our model finds time varying dynamics when
applied to real fMRI data.
Comparison with Existing Method(s): The proposed model is better at detecting
activity in simulated data than standard models, without inflating the false
positive rate. When applied to real fMRI data, our GP model in several cases
finds brain activity where previously proposed LTI models does not.
Conclusions: We have proposed a new non-linear model for the hemodynamics in
task fMRI, that is able to detect active voxels, and gives the opportunity to
ask new kinds of questions related to hemodynamics.Comment: 18 pages, 14 figure
Nonparametric Modeling of Dynamic Functional Connectivity in fMRI Data
Dynamic functional connectivity (FC) has in recent years become a topic of
interest in the neuroimaging community. Several models and methods exist for
both functional magnetic resonance imaging (fMRI) and electroencephalography
(EEG), and the results point towards the conclusion that FC exhibits dynamic
changes. The existing approaches modeling dynamic connectivity have primarily
been based on time-windowing the data and k-means clustering. We propose a
non-parametric generative model for dynamic FC in fMRI that does not rely on
specifying window lengths and number of dynamic states. Rooted in Bayesian
statistical modeling we use the predictive likelihood to investigate if the
model can discriminate between a motor task and rest both within and across
subjects. We further investigate what drives dynamic states using the model on
the entire data collated across subjects and task/rest. We find that the number
of states extracted are driven by subject variability and preprocessing
differences while the individual states are almost purely defined by either
task or rest. This questions how we in general interpret dynamic FC and points
to the need for more research on what drives dynamic FC.Comment: 8 pages, 1 figure. Presented at the Machine Learning and
Interpretation in Neuroimaging Workshop (MLINI-2015), 2015 (arXiv:1605.04435
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
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