1,616 research outputs found
Adaptive Smoothing in fMRI Data Processing Neural Networks
Functional Magnetic Resonance Imaging (fMRI) relies on multi-step data
processing pipelines to accurately determine brain activity; among them, the
crucial step of spatial smoothing. These pipelines are commonly suboptimal,
given the local optimisation strategy they use, treating each step in
isolation. With the advent of new tools for deep learning, recent work has
proposed to turn these pipelines into end-to-end learning networks. This change
of paradigm offers new avenues to improvement as it allows for a global
optimisation. The current work aims at benefitting from this paradigm shift by
defining a smoothing step as a layer in these networks able to adaptively
modulate the degree of smoothing required by each brain volume to better
accomplish a given data analysis task. The viability is evaluated on real fMRI
data where subjects did alternate between left and right finger tapping tasks.Comment: 4 pages, 3 figures, 1 table, IEEE 2017 International Workshop on
Pattern Recognition in Neuroimaging (PRNI
Adaptive Gaussian Markov Random Fields with Applications in Human Brain Mapping
Functional magnetic resonance imaging (fMRI) has become the standard technology in human brain mapping. Analyses of the massive spatio-temporal fMRI data sets often focus on parametric or nonparametric modeling of the temporal component, while spatial smoothing is based on Gaussian kernels or random fields. A weakness of Gaussian spatial smoothing is underestimation of activation peaks or blurring of high-curvature transitions between activated and non-activated brain regions. In this paper, we introduce a class of inhomogeneous Markov random fields (MRF) with spatially adaptive interaction weights in a space-varying coefficient model for fMRI data. For given weights, the random field is conditionally Gaussian, but marginally it is non-Gaussian. Fully Bayesian inference, including estimation of weights and variance parameters, is carried out through efficient MCMC simulation. An application to fMRI data from a visual stimulation experiment demonstrates the performance of our approach in comparison to Gaussian and robustified non-Gaussian Markov random field models
Structural adaptive smoothing: Principles and applications in imaging
Structural adaptive smoothing provides a new concept of edge-preserving non-parametric smoothing methods. In imaging it employs qualitative assumption on the underlying homogeneity structure of the image. The chapter describes the main principles of the approach and discusses applications ranging from image denoising to the analysis of functional and diffusion weighted Magnetic Resonance experiments
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
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Statistical parametric maps for functional MRI experiments in R: the package fmri
The package fmri is provided for analysis of single run functional
Magnetic Resonance Imaging data. It implements structural adaptive smoothing
methods with signal detection for adaptive noise reduction which avoids
blurring of edges of activation areas. fmri provides fmri analysis from time
series modeling to signal detection and publication-ready image
Statistical parametric maps for functional MRI experiments in R: The package fmri
The package fmri is provided for analysis of single run functional Magnetic Resonance Imaging data. It implements structural adaptive smoothing methods with signal detection for adaptive noise reduction which avoids blurring of edges of activation areas. fmri provides fmri analysis from time series modeling to signal detection and publication-ready images
Structural Adaptive Smoothing in Diffusion Tensor Imaging: The R Package dti
Diffusion weighted imaging has become and will certainly continue to be an important tool in medical research and diagnostics. Data obtained with diffusion weighted imaging are characterized by a high noise level. Thus, estimation of quantities like anisotropy indices or the main diffusion direction may be significantly compromised by noise in clinical or neuroscience applications. Here, we present a new package dti for R, which provides functions for the analysis of diffusion weighted data within the diffusion tensor model. This includes smoothing by a recently proposed structural adaptive smoothing procedure based on the propagation-separation approach in the context of the widely used diffusion tensor model. We extend the procedure and show, how a correction for Rician bias can be incorporated. We use a heteroscedastic nonlinear regression model to estimate the diffusion tensor. The smoothing procedure naturally adapts to different structures of different size and thus avoids oversmoothing edges and fine structures. We illustrate the usage and capabilities of the package through some examples.
Structural adaptive smoothing for single-subject analysis in SPM: the aws4SPM-toolbox
There exists a variety of software tools for analyzing functional Magnetic Resonance Imaging data. A very popular one is the freely available SPM package by the Functional Imaging Laboratory at the Wellcome Department of Imaging Neuroscience. In order to enhance the signal-to-noise ratio it provides the possibility to smooth the data in a pre-processing step by a Gaussian filter. However, this comes at the cost of reducing the effective resolution. In a series of recent papers it has been shown, that using a structural adaptive smoothing algorithm based on the Propagation-Separation method allows for enhanced signal detection while preserving the shape and spatial extent of the activation areas. Here, we describe our implementation of this algorithm as a toolbox for SPM
Adaptive smoothing as inference strategy: More specificity for unequally sized or neighboring regions
Although spatial smoothing of fMRI data can serve multiple purposes, increasing
the sensitivity of activation detection is probably its greatest benefit.
However, this increased detection power comes with a loss of specificity when
non-adaptive smoothing (i.e.\ the standard in most software packages) is used.
Simulation studies and analysis of experimental data was performed using the
R packages neuRosim and fmri. In these studies, we
systematically investigated the effect of spatial smoothing on the power and
number of false positives in two particular cases that are often encountered in
fMRI research: (1) Single condition activation detection for regions that differ
in size, and (2) multiple condition activation detection for neighbouring
regions. Our results demonstrate that adaptive smoothing is superior in both
cases because less false positives are introduced by the spatial smoothing
process compared to standard Gaussian smoothing or FDR inference of unsmoothed
data
High resolution fMRI: Overcoming the signal-to-noise problem
Increasing the spatial resolution in functional Magnetic Resonance Imaging (fMRI) inherently lowers the signal-to-noise ratio (SNR). In order to still detect functionally significant activations in high-resolution images, spatial smoothing of the data is required. However, conventional non-adaptive smoothing comes with a reduced effective resolution, foiling the benefit of the higher acquisition resolution. We show how our recently proposed structural adaptive smoothing procedure for functional MRI data can improve signal detection of high-resolution fMRI experiments regardless of the lower SNR. The procedure is evaluated on human visual and sensory-motor mapping experiments. In these applications, the higher resolution could be fully utilized and high-resolution experiments were outperforming normal resolution experiments by means of both statistical significance and information content
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