Synthetic Magnetic Resonance Imaging Revisited

Synthetic magnetic resonance (MR) imaging is an approach suggested in the literature to predict MR images at different design parameter settings from at least three observed MR scans. However, performance is poor when no regularization is used in the estimation and otherwise computationally impractical to implement for three-dimensional imaging methods. We propose a method which accounts for spatial context in MR images by the imposition of a Gaussian Markov Random Field (MRF) structure on a transformation of the spin-lattice relaxation time, the spin-spin relaxation time and the proton density at each voxel. The MRF structure is specified through a Matrix Normal distribution. We also model the observed magnitude images using the more accurate but computationally challenging Rice distribution. A One-Step-Late Expectation-Maximization approach is adopted to make our approach computationally practical. We evaluate predictive performance in generating synthetic MR images in a clinical setting: our results indicate that our suggested approach is not only computationally feasible to implement but also shows excellent performance

SynMRI: An R Package for Synthetic Magnetic Resonance Imaging

Synthetic magnetic resonance (MR) imaging refers to the procedure used to predict magnetic resonance images for any given design parameter settings using at least three observed MRI scans. SynMRI is an R packaged we developed for this purpose. We implemented the method proposed in Maitra and Riddles (2010), which used a model based on the Bloch equation, an empirical expression describing the nuclear magnetic resonance phenomena, to get voxel-wise estimates that are used to predict the intensity values for a given design parameters settings. The noise on the MR signal is modeled using the Rice distribution. All the parameters involved are estimated using the EM algorithm. SynMRI includes functions the compute the estimates, and visualize and evaluate the results. The EM algorithm estimation stage is performed in C since it is the part most compute intensive

Model-based Personalized Synthetic MR Imaging

Synthetic Magnetic Resonance (MR) imaging predicts images at new design parameter settings from a few observed MR scans. Model-based methods, that use both the physical and statistical properties underlying the MR signal and its acquisition, can predict images at any setting from as few as three scans, allowing it to be used in individualized patient- and anatomy-specific contexts. However, the estimation problem in model-based synthetic MR imaging is ill-posed and so regularization, in the form of correlated Gaussian Markov Random Fields, is imposed on the voxel-wise spin-lattice relaxation time, spin-spin relaxation time and the proton density underlying the MR image. We develop theoretically sound but computationally practical matrix-free estimation methods for synthetic MR imaging. Our evaluations demonstrate excellent ability of our methods to synthetize MR images in a clinical framework and also estimation and prediction accuracy and consistency. An added strength of our model-based approach, also developed and illustrated here, is the accurate estimation of standard errors of regional means in the synthesized images.Comment: 13 pages, 5 figures, 5 table

On the Expectation-Maximization Algorithm for Rice-Rayleigh Mixtures With Application to Noise Parameter Estimation in Magnitude MR Datasets

Magnitude magnetic resonance (MR) images are noise-contaminated measurements of the true signal, and it is important to assess the noise in many applications. A recently introduced approach models the magnitude MR datum at each voxel in terms of a mixture of upto one Rayleigh and an a priori unspecified number of Rice components, all with a common noise parameter. The Expectation-Maximization (EM) algorithm was developed for parameter estimation, with the mixing component membership of each voxel as the missing observation. This paper revisits the EM algorithm by introducing more missing observations into the estimation problem such that the complete (observed and missing parts) dataset can be modeled in terms of a regular exponential family. Both the EM algorithm and variance estimation are then fairly straightforward without any need for potentially unstable numerical optimization methods. Compared to local neighborhood- and wavelet-based noise-parameter estimation methods, the new EMbased approach is seen to perform well not only on simulation datasets but also on physical phantom and clinical imaging data

Extended Modality Propagation: Image Synthesis of Pathological Cases

International audienceThis paper describes a novel generative model for the synthesis of multi-modal medical images of pathological cases based on a single label map. Our model builds upon i) a generative model commonly used for label fusion and multi-atlas patch-based segmentation of healthy anatomical structures, ii) the Modality Propagation iterative strategy used for a spatially-coherent synthesis of subject-specific scans of desired image modalities. The expression Extended Modality Propagation is coined to refer to the extension of Modality Propagation to the synthesis of images of pathological cases. Moreover, image synthesis uncertainty is estimated. An application to Magnetic Resonance Imaging synthesis of glioma-bearing brains is i) validated on the training dataset of a Multimodal Brain Tumor Image Segmentation challenge, ii) compared to the state-of-the-art in glioma image synthesis, and iii) illustrated using the output of two different tumor growth models. Such a generative model allows the generation of a large dataset of synthetic cases, which could prove useful for the training, validation, or benchmarking of image processing algorithms

Bayesian generative learning of brain and spinal cord templates from neuroimaging datasets

In the field of neuroimaging, Bayesian modelling techniques have been largely adopted and recognised as powerful tools for the purpose of extracting quantitative anatomical and functional information from medical scans. Nevertheless the potential of Bayesian inference has not yet been fully exploited, as many available tools rely on point estimation techniques, such as maximum likelihood estimation, rather than on full Bayesian inference. The aim of this thesis is to explore the value of approximate learning schemes, for instance variational Bayes, to perform inference from brain and spinal cord MRI data. The applications that will be explored in this work mainly concern image segmentation and atlas construction, with a particular emphasis on the problem of shape and intensity prior learning, from large training data sets of structural MR scans. The resulting computational tools are intended to enable integrated brain and spinal cord morphometric analyses, as opposed to the approach that is most commonly adopted in neuroimaging, which consists in optimising separate tools for brain and spine morphometrics

Synthetic Magnetic Resonance Imaging Revisited

Synthetic magnetic resonance (MR) imaging is an approach suggested in the literature to predict MR images at different design parameter settings from at least three observed MR scans. However, performance is poor when no regularization is used in the estimation and otherwise computationally impractical to implement for three-dimensional imaging methods. We propose a method which accounts for spatial context in MR images by the imposition of a Gaussian Markov Random Field (MRF) structure on a transformation of the spin-lattice relaxation time, the spin-spin relaxation time and the proton density at each voxel. The MRF structure is specified through a Matrix Normal distribution. We also model the observed magnitude images using the more accurate but computationally challenging Rice distribution. A One-Step-Late Expectation-Maximization approach is adopted to make our approach computationally practical. We evaluate predictive performance in generating synthetic MR images in a clinical setting: our results indicate that our suggested approach is not only computationally feasible to implement but also shows excellent performance.This is a manuscript of an article from IEEE Transactions on Medical Imaging 29 (2010): 895, doi: 10.1109/TMI.2009.2039487. Posted with permission. Copyright 2010 IEEE.</p