A R-Script for Generating Multiple Sclerosis Lesion Pattern Discrimination Plots

Càlcul estadístic R; Geoestadística; Esclerosi múltipleCálculo estadístico R; Geoestadística; Esclerosis múltipleR statistical computing; Geostatistics; Multiple sclerosisOne significant characteristic of Multiple Sclerosis (MS), a chronic inflammatory demyelinating disease of the central nervous system, is the evolution of highly variable patterns of white matter lesions. Based on geostatistical metrics, the MS-Lesion Pattern Discrimination Plot reduces complex three- and four-dimensional configurations of MS-White Matter Lesions to a well-arranged and standardized two-dimensional plot that facilitates follow-up, cross-sectional and medication impact analysis. Here, we present a script that generates the MS-Lesion Pattern Discrimination Plot, using the widespread statistical computing environment R. Input data to the script are Nifti-1 or Analyze-7.5 files with individual MS-White Matter Lesion masks in Montreal Normal Brain geometry. The MS-Lesion Pattern Discrimination Plot, variogram plots and associated fitting statistics are output to the R console and exported to standard graphics and text files. Besides reviewing relevant geostatistical basics and commenting on implementation details for smooth customization and extension, the paper guides through generating MS-Lesion Pattern Discrimination Plots using publicly available synthetic MS-Lesion patterns. The paper is accompanied by the R script LDPgenerator.r, a small sample data set and associated graphics for comparison

A MS-lesion pattern discrimination plot based on geostatistics

Introduction A geostatistical approach to characterize MS-lesion patterns based on their geometrical properties is presented. Methods A dataset of 259 binary MS-lesion masks in MNI space was subjected to directional variography. A model function was fit to express the observed spatial variability in x, y, z directions by the geostatistical parameters Range and Sill. Results Parameters Range and Sill correlate with MS-lesion pattern surface complexity and total lesion volume. A scatter plot of ln(Range) versus ln(Sill), classified by pattern anisotropy, enables a consistent and clearly arranged presentation of MS-lesion patterns based on geometry: the so-called MS-Lesion Pattern Discrimination Plot. Conclusions The geostatistical approach and the graphical representation of results are considered efficient exploratory data analysis tools for cross-sectional, follow-up, and medication impact analysis

Geostatistical Analysis of White Matter Lesions in Multiple Sclerosis Identifies Gender Differences in Lesion Evolution

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system with presumed autoimmune origin. The development of lesions within the gray matter and white matter, which are highly variable with respect to number, total volume, morphology and spatial evolution and which only show a limited correlation with clinical disability, is a hallmark of the disease. Population-based studies indicate a distinct outcome depending on gender. Here, we studied gender-related differences in the evolution of white matter MS-lesions (MS-WML) in early MS by using geostatistical methods. Within a 3 years observation period, a female and a male MS patient group received disease modifying drugs and underwent standardized annual brain magnetic resonance imaging, accompanied by neurological examination. MS-WML were automatically extracted and the derived binary lesion masks were subject to geostatistical analysis, yielding quantitative spatial-statistics metrics on MS-WML pattern morphology and total lesion volume (TLV). Through the MS-lesion pattern discrimination plot, the following differences were disclosed: corresponding to gender and MS-WML pattern morphology at baseline, two female subgroups (F1, F2) and two male subgroups (M1, M2) are discerned that follow a distinct MS-WML pattern evolution in space and time. F1 and M1 start with medium-level MS-WML pattern smoothness and TLV, both behave longitudinally quasi-static. By contrast, F2 and M2 start with high-level MS-WML pattern smoothness and medium-level TLV. F2 and M2 longitudinal development is characterized by strongly diminishing MS-WML pattern smoothness and TLV, i.e., continued shrinking and break-up of MS-WML. As compared to the male subgroup M2, the female subgroup F2 shows continued, increased MS-WML pattern smoothness and TLV. Data from neurological examination suggest a correlation of MS-WML pattern morphology metrics and EDSS. Our results justify detailed studies on gender-related differences

Across Space and Time. Papers from the 41st Conference on Computer Applications and Quantitative Methods in Archaeology, Perth, 25-28 March 2013

This volume presents a selection of the best papers presented at the forty-first annual Conference on Computer Applications and Quantitative Methods in Archaeology. The theme for the conference was "Across Space and Time", and the papers explore a multitude of topics related to that concept, including databases, the semantic Web, geographical information systems, data collection and management, and more

Spatial statistics and analysis of earth's ionosphere

Thesis (Ph.D.)--Boston UniversityThe ionosphere, a layer of Earths upper atmosphere characterized by energetic charged particles, serves as a natural plasma laboratory and supplies proxy diagnostics of space weather drivers in the magnetosphere and the solar wind. The ionosphere is a highly dynamic medium, and the spatial structure of observed features (such as auroral light emissions, charge density, temperature, etc.) is rich with information when analyzed in the context of fluid, electromagnetic, and chemical models. Obtaining measurements with higher spatial and temporal resolution is clearly advantageous. For instance, measurements obtained with a new electronically-steerable incoherent scatter radar (ISR) present a unique space-time perspective compared to those of a dish-based ISR. However, there are unique ambiguities for this modality which must be carefully considered. The ISR target is stochastic, and the fidelity of fitted parameters (ionospheric densities and temperatures) requires integrated sampling, creating a tradeoff between measurement uncertainty and spatio-temporal resolution. Spatial statistics formalizes the relationship between spatially dispersed observations and the underlying process(es) they represent. A spatial process is regarded as a random field with its distribution structured (e.g., through a correlation function) such that data, sampled over a spatial domain, support inference or prediction of the process. Quantification of uncertainty, an important component of scientific data analysis, is a core value of spatial statistics. This research applies the formalism of spatial statistics to the analysis of Earth's ionosphere using remote sensing diagnostics. In the first part, we consider the problem of volumetric imaging using phased-array ISR based on optimal spatial prediction ("kriging"). In the second part, we develop a technique for reconstructing two-dimensional ion flow fields from line-of-sight projections using Tikhonov regularization. In the third part, we adapt our spatial statistical approach to global ionospheric imaging using total electron content (TEC) measurements derived from navigation satellite signals

Across Space and Time Papers from the 41st Conference on Computer Applications and Quantitative Methods in Archaeology, Perth, 25-28 March 2013

The present volume includes 50 selected peer-reviewed papers presented at the 41st Computer Applications and Quantitative Methods in Archaeology Across Space and Time (CAA2013) conference held in Perth (Western Australia) in March 2013 at the University Club of Western Australia and hosted by the recently established CAA Australia National Chapter. It also hosts a paper presented at the 40th Computer Applications and Quantitative Methods in Archaeology (CAA2012) conference held in Southampton