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.

Data augmentation in Rician noise model and Bayesian Diffusion Tensor Imaging

Mapping white matter tracts is an essential step towards understanding brain function. Diffusion Magnetic Resonance Imaging (dMRI) is the only noninvasive technique which can detect in vivo anisotropies in the 3-dimensional diffusion of water molecules, which correspond to nervous fibers in the living brain. In this process, spectral data from the displacement distribution of water molecules is collected by a magnetic resonance scanner. From the statistical point of view, inverting the Fourier transform from such sparse and noisy spectral measurements leads to a non-linear regression problem. Diffusion tensor imaging (DTI) is the simplest modeling approach postulating a Gaussian displacement distribution at each volume element (voxel). Typically the inference is based on a linearized log-normal regression model that can fit the spectral data at low frequencies. However such approximation fails to fit the high frequency measurements which contain information about the details of the displacement distribution but have a low signal to noise ratio. In this paper, we directly work with the Rice noise model and cover the full range of $b$-values. Using data augmentation to represent the likelihood, we reduce the non-linear regression problem to the framework of generalized linear models. Then we construct a Bayesian hierarchical model in order to perform simultaneously estimation and regularization of the tensor field. Finally the Bayesian paradigm is implemented by using Markov chain Monte Carlo.Comment: 37 pages, 3 figure

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

Parameter optimization for local polynomial approximation based intersection confidence interval filter using genetic algorithm: an application for brain MRI image de-noising

Magnetic resonance imaging (MRI) is extensively exploited for more accuratepathological changes as well as diagnosis. Conversely, MRI suffers from variousshortcomings such as ambient noise from the environment, acquisition noise from theequipment, the presence of background tissue, breathing motion, body fat, etc.Consequently, noise reduction is critical as diverse types of the generated noise limit the efficiency of the medical image diagnosis. Local polynomial approximation basedintersection confidence interval (LPA-ICI) filter is one of the effective de-noising filters.This filter requires an adjustment of the ICI parameters for efficient window size selection.From the wide range of ICI parametric values, finding out the best set of tunes values is itselfan optimization problem. The present study proposed a novel technique for parameteroptimization of LPA-ICI filter using genetic algorithm (GA) for brain MR imagesde-noising. The experimental results proved that the proposed method outperforms theLPA-ICI method for de-noising in terms of various performance metrics for different noisevariance levels. Obtained results reports that the ICI parameter values depend on the noisevariance and the concerned under test image

Blind restoration of images with penalty-based decision making : a consensus approach

In this thesis we show a relationship between fuzzy decision making and image processing . Various applications for image noise reduction with consensus methodology are introduced. A new approach is introduced to deal with non-stationary Gaussian noise and spatial non-stationary noise in MRI

Denoising magnetic resonance images using collaborative non-local means

Noise artifacts in magnetic resonance (MR) images increase the complexity of image processing workflows and decrease the reliability of inferences drawn from the images. It is thus often desirable to remove such artifacts beforehand for more robust and effective quantitative analysis. It is important to preserve the integrity of relevant image information while removing noise in MR images. A variety of approaches have been developed for this purpose, and the non-local means (NLM) filter has been shown to be able to achieve state-of-the-art denoising performance. For effective denoising, NLM relies heavily on the existence of repeating structural patterns, which however might not always be present within a single image. This is especially true when one considers the fact that the human brain is complex and contains a lot of unique structures. In this paper we propose to leverage the repeating structures from multiple images to collaboratively denoise an image. The underlying assumption is that it is more likely to find repeating structures from multiple scans than from a single scan. Specifically, to denoise a target image, multiple images, which may be acquired from different subjects, are spatially aligned to the target image, and an NLM-like block matching is performed on these aligned images with the target image as the reference. This will significantly increase the number of matching structures and thus boost the denoising performance. Experiments on both synthetic and real data show that the proposed approach, collaborative non-local means (CNLM), outperforms the classic NLM and yields results with markedly improved structural details

Sparse Representation-Based Framework for Preprocessing Brain MRI

This thesis addresses the use of sparse representations, specifically Dictionary Learning and Sparse Coding, for pre-processing brain MRI, so that the processed image retains the fine details of the original image, to improve the segmentation of brain structures, to assess whether there is any relationship between alterations in brain structures and the behavior of young offenders. Denoising an MRI while keeping fine details is a difficult task; however, the proposed method, based on sparse representations, NLM, and SVD can filter noise while prevents blurring, artifacts, and residual noise. Segmenting an MRI is a non-trivial task; because normally the limits between regions in these images may be neither clear nor well defined, due to the problems which affect MRI. However, this method, from both the label matrix of the segmented MRI and the original image, yields a new improved label matrix in which improves the limits among regions.DoctoradoDoctor en Ingeniería de Sistemas y Computació