ROC performance evaluation of RADSPM technique

The purpose of Functional Magnetic Resonance Imaging (fMRI) is to map areas of increased neuronal activity of the human brain. fMRI has been applied to investigate a variety of neuronal processes from activities in the primary sensory and motor cortices to cognitive functions such as perception or learning. Robust anisotropic diffusion of statistical parametric maps (RADSPM) is a new technique to improve functional Magnetic Resonance Imaging. RADSPM attempts to improve voxel classification based on robust anisotropic diffusion (RAD) to include the spatial relationship between active voxels. This paper compares two fMRI postprocessing techniques used to identify areas of increased neuronal activity, a widely used method, correlation analysis, and RADSPM. In recent years, the use of ROC analysis has been extended from its original use in communication systems to machine learning, pattern classification and fMRI. We proposed to use ROC curves and the area under the curve (AUC) not only as a final performance evaluation and visualizing technique but as a gauging parameter procedure in RADSPM. We give a brief review of the main methods and conclude presenting experimental results and suggesting further research alternatives.Workshop de Computación Gráfica, Imágenes y Visualización (WCGIV)Red de Universidades con Carreras en Informática (RedUNCI

Effects of Non-Local Diffusion on Structural MRI Preprocessing and Default Network Mapping: Statistical Comparisons with Isotropic/Anisotropic Diffusion

Neuroimaging community usually employs spatial smoothing to denoise magnetic resonance imaging (MRI) data, e.g., Gaussian smoothing kernels. Such an isotropic diffusion (ISD) based smoothing is widely adopted for denoising purpose due to its easy implementation and efficient computation. Beyond these advantages, Gaussian smoothing kernels tend to blur the edges, curvature and texture of images. Researchers have proposed anisotropic diffusion (ASD) and non-local diffusion (NLD) kernels. We recently demonstrated the effect of these new filtering paradigms on preprocessing real degraded MRI images from three individual subjects. Here, to further systematically investigate the effects at a group level, we collected both structural and functional MRI data from 23 participants. We first evaluated the three smoothing strategies' impact on brain extraction, segmentation and registration. Finally, we investigated how they affect subsequent mapping of default network based on resting-state functional MRI (R-fMRI) data. Our findings suggest that NLD-based spatial smoothing maybe more effective and reliable at improving the quality of both MRI data preprocessing and default network mapping. We thus recommend NLD may become a promising method of smoothing structural MRI images of R-fMRI pipeline

ROC performance evaluation of RADSPM technique

The purpose of Functional Magnetic Resonance Imaging (fMRI) is to map areas of increased neuronal activity of the human brain. fMRI has been applied to investigate a variety of neuronal processes from activities in the primary sensory and motor cortices to cognitive functions such as perception or learning. Robust anisotropic diffusion of statistical parametric maps (RADSPM) is a new technique to improve functional Magnetic Resonance Imaging. RADSPM attempts to improve voxel classification based on robust anisotropic diffusion (RAD) to include the spatial relationship between active voxels. This paper compares two fMRI postprocessing techniques used to identify areas of increased neuronal activity, a widely used method, correlation analysis, and RADSPM. In recent years, the use of ROC analysis has been extended from its original use in communication systems to machine learning, pattern classification and fMRI. We proposed to use ROC curves and the area under the curve (AUC) not only as a final performance evaluation and visualizing technique but as a gauging parameter procedure in RADSPM. We give a brief review of the main methods and conclude presenting experimental results and suggesting further research alternatives.Workshop de Computación Gráfica, Imágenes y Visualización (WCGIV)Red de Universidades con Carreras en Informática (RedUNCI

Diffuse outlier time series detection technique for functional magnetic resonance imaging

We propose a new support vector machine (SVM) based method that improves the time series classi cation in magnetic resonance imaging (fMRI). We exploit the robust anisotropic di usion (RAD) technique to increase the classi cation performance of the one class support vector machine by taking into account the hypothesis of spatial relationship between active voxels. The proposed method was called Di use One Class Support Vector Machine (DOCSVM). DOCSVM method treats activated voxels as outliers and applies one class support vector machine to generate an activation map and RAD to include the neighborhood hypothesis, improving the classi cation and reducing the iteration steps with respect to RADSPM. We give a brief review of the main methods, present receiver operating characteristic (ROC) results and conclude suggesting further research alternatives.Presentado en el I Workshop Procesamiento de señales y Sistemas de Tiempo Real (WPSTR)Red de Universidades con Carreras en Informática (RedUNCI

Scaling Multidimensional Inference for Big Structured Data

In information technology, big data is a collection of data sets so large and complex that it becomes difficult to process using traditional data processing applications [151]. In a world of increasing sensor modalities, cheaper storage, and more data oriented questions, we are quickly passing the limits of tractable computations using traditional statistical analysis methods. Methods which often show great results on simple data have difficulties processing complicated multidimensional data. Accuracy alone can no longer justify unwarranted memory use and computational complexity. Improving the scaling properties of these methods for multidimensional data is the only way to make these methods relevant. In this work we explore methods for improving the scaling properties of parametric and nonparametric models. Namely, we focus on the structure of the data to lower the complexity of a specific family of problems. The two types of structures considered in this work are distributive optimization with separable constraints (Chapters 2-3), and scaling Gaussian processes for multidimensional lattice input (Chapters 4-5). By improving the scaling of these methods, we can expand their use to a wide range of applications which were previously intractable open the door to new research questions

MP-PCA denoising of fMRI time-series data can lead to artificial activation "spreading"

MP-PCA denoising has become the method of choice for denoising in MRI since it provides an objective threshold to separate the desired signal from unwanted thermal noise components. In rodents, thermal noise in the coils is an important source of noise that can reduce the accuracy of activation mapping in fMRI. Further confounding this problem, vendor data often contains zero-filling and other effects that may violate MP-PCA assumptions. Here, we develop an approach to denoise vendor data and assess activation "spreading" caused by MP-PCA denoising in rodent task-based fMRI data. Data was obtained from N = 3 mice using conventional multislice and ultrafast acquisitions (1 s and 50 ms temporal resolution, respectively), during visual stimulation. MP-PCA denoising produced SNR gains of 64% and 39% and Fourier spectral amplitude (FSA) increases in BOLD maps of 9% and 7% for multislice and ultrafast data, respectively, when using a small [2 2] denoising window. Larger windows provided higher SNR and FSA gains with increased spatial extent of activation that may or may not represent real activation. Simulations showed that MP-PCA denoising causes activation "spreading" with an increase in false positive rate and smoother functional maps due to local "bleeding" of principal components, and that the optimal denoising window for improved specificity of functional mapping, based on Dice score calculations, depends on the data's tSNR and functional CNR. This "spreading" effect applies also to another recently proposed low-rank denoising method (NORDIC). Our results bode well for dramatically enhancing spatial and/or temporal resolution in future fMRI work, while taking into account the sensitivity/specificity trade-offs of low-rank denoising methods

An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies

Diffusion-based spatial priors for imaging.

We describe a Bayesian scheme to analyze images, which uses spatial priors encoded by a diffusion kernel, based on a weighted graph Laplacian. This provides a general framework to formulate a spatial model, whose parameters can be optimised. The standard practice using the software statistical parametric mapping (SPM) is to smooth imaging data using a fixed Gaussian kernel as a pre-processing step before applying a mass-univariate statistical model (e.g., a general linear model) to provide images of parameter estimates (Friston et al., 2006). This entails the strong assumption that data are generated smoothly throughout the brain. An alternative is to include smoothness in a multivariate statistical model (Penny et al., 2005). The advantage of the latter is that each parameter field is smoothed automatically, according to a measure of uncertainty, given the data. Explicit spatial priors enable formal model comparison of different prior assumptions, e.g. that data are generated from a stationary (i.e. fixed throughout the brain) or non-stationary spatial process. We describe the motivation, background material and theory used to formulate diffusion-based spatial priors for fMRI data and apply it to three different datasets, which include standard and high-resolution data. We compare mass-univariate ordinary least squares estimates of smoothed data and three Bayesian models spatially independent, stationary and non-stationary spatial models of non-smoothed data. The latter of which can be used to preserve boundaries between functionally selective regional responses of the brain, thereby increasing the spatial detail of inferences about cortical responses to experimental input