92C55 Biomedical imaging and signal processing [See also 44A12, 65R10]
Refine
Language
- English (5)
Keywords
- spatially adaptive smoothing (3)
- functional MRI (2)
- signal detection (2)
- Diffusion tensor imaging (1)
- Functional Magnetic Resonance Imaging (1)
- Image Enhancement (1)
- Multiscale Testing (1)
- NeuroImaging (1)
- R (1)
- Structural Adaptive Smoothing (1)
R is a language and environment for statistical computing and graphics. It can be considered an alternative implementation of the S language developed in the 1970s and 1980s for data analysis and graphics (Becker and Chambers, 1984; Becker et al., 1988). The R language is part of the GNU project and offers versions that compile and run on almost every major operating system currently available. We highlight several R packages built specifically for the analysis of neuroimaging data in the context of functional MRI, diffusion tensor imaging, and dynamic contrast-enhanced MRI. We review their methodology and give an overview of their capabilities for neuroimaging. In addition we summarize some of the current activities in the area of neuroimaging software development in R.
Functional Magnetic Resonance Imaging inherently involves noisy measurements and a severe multiple test
problem. Smoothing is usually used to reduce the effective number of multiple
comparisons and to locally integrate the signal and hence increase the
signal-to-noise ratio. Here, we provide a new structural adaptive segmentation
algorithm (AS)
that naturally combines the signal detection with noise reduction in one procedure.
Moreover, the new method
is closely related to a recently proposed structural adaptive smoothing
algorithm and preserves shape and spatial extent of activation areas without
blurring the borders.
Diffusion Tensor Imaging (DTI) data is characterized by a high noise level. Thus,
estimation errors of quantities like anisotropy indices or the main diffusion direction
used for fiber tracking are relatively large and may significantly confound the accuracy
of DTI in clinical or neuroscience applications. Besides pulse sequence optimization,
noise reduction by smoothing the data can be pursued as a complementary approach
to increase the accuracy of DTI. Here, we suggest an anisotropic structural adaptive
smoothing procedure, which is based on the Propagation-Separation method and preserves
the structures seen in DTI and their different sizes and shapes. It is applied
to artificial phantom data and a brain scan. We show that this method significantly
improves the quality of the estimate of the diffusion tensor and hence enables one
either to reduce the number of scans or to enhance the input for subsequent analysis
such as fiber tracking.
An important problem of the analysis of fMRI experiments is to achieve some noise reduction of the data without blurring the shape of the activation areas. As a novel solution to this problem, the Propagation-Separation approach (PS), a structure adaptive smoothing method, has been proposed recently. PS adapts to different shapes of activation areas by generating a spatial structure corresponding to similarities and differences between time series in adjacent locations. In this paper we demonstrate how this method results in more accurate localization of brain activity. First, it is shown in numerical simulations that PS is superior over Gaussian smoothing with respect to the accurate description of the shape of activation clusters and and results in less false detections. Second, in a study of 37 presurgical planning cases we found that PS and Gaussian smoothing often yield different results, and we present examples showing aspects of the superiority of PS as applied to presurgical planning.
Data from functional magnetic resonance imaging (fMRI) consists of time series of brain images which are characterized
by a high noise level and a low signal-to-noise ratio. We provide a complete procedure for fMRI analysis. In order to reduce noise and to improve signal detection the fMRI data is spatially smoothed. However, the common application of a Gaussian filter does this at the cost of loss of information on spatial extend and shape of the activation area. We suggest to use the propagation-separation procedures introduced by Polzehl and Spokoiny (2005) instead. We show that this significantly improves the information on the spatial extend and shape of the activation region with similar results for the noise reduction. Signal detection is based on locally varying thresholds defined by random field theory. Effects of adaptive and non adaptive smoothing are illustrated by artificial examples and an analysis of real data.