Filters

More filters

2019 - 2019272020 - 20223
Reset filters

Settings

Author: Tabelow, Karsten × Type: Report ×

Search Results

Now showing 1 - 10 of 30
  • Thumbnail Image
    Item
    Adaptive smoothing as inference strategy: More specificity for unequally sized or neighboring regions
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2013) Welvaert, Marijke; Tabelow, Karsten; Seurinck, Ruth; Rosseel, Yves
    Although spatial smoothing of fMRI data can serve multiple purposes, increasing the sensitivity of activation detection is probably its greatest benefit. However, this increased detection power comes with a loss of specificity when non-adaptive smoothing (i.e. the standard in most software packages) is used. Simulation studies and analysis of experimental data was performed using the R packages neu-Rosim and fmri. In these studies, we systematically investigated the effect of spatial smoothing on the power and number of false positives in two particular cases that are often encountered in fMRI research: (1) Single condition activation detection for regions that differ in size, and (2) multiple condition activation detection for neighbouring regions. Our results demonstrate that adaptive smoothing is superior in both cases because less false positives are introduced by the spatial smoothing process compared to standard Gaussian smoothing or FDR inference of unsmoothed data.
  • Thumbnail Image
    Item
    Modeling high resolution MRI: Statistical issues with low SNR
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2015) Polzehl, Jörg; Tabelow, Karsten
    Noise is a common issue for all Magnetic Resonance Imaging (MRI) techniques and obviously leads to variability of the estimates in any model describing the data. A number of special MR sequences as well as increasing spatial resolution in MR experiments further diminish the signal-to-noise ratio (SNR). However, with low SNR the expected signal deviates from its theoretical value. Common modeling approaches therefore lead to a bias in estimated model parameters. Adjustments require an analysis of the data generating process and a characterization of the resulting distribution of the imaging data. We provide an adequate quasi-likelihood approach that employs these characteristics. We elaborate on the effects of typical data preprocessing and analyze the bias effects related to low SNR for the example of the diffusion tensor model in diffusion MRI. We then demonstrate that the problem is relevant even for data from the Human Connectome Project, one of the highest quality diffusion MRI data available so far.
  • Thumbnail Image
    Item
    Improving accuracy and temporal resolution of learning curve estimation for within- and across-session analysis
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2015) Deliano, Matthias; Tabelow, Karsten; König, Reinhard; Polzehl, Jörg
    Estimation of learning curves is ubiquitously based on proportions of correct responses within moving trial windows. In this approach, it is tacitly assumed that learning performance is constant within the moving windows, which, however, is often not the case. In the present study we demonstrate that violations of this assumption lead to systematic errors in the analysis of learning curves, and we explored the dependency of these errors on window size, different statistical models, and learning phase. To reduce these errors for single subjects as well as on the population level, we propose adequate statistical methods for the estimation of learning curves and the construction of confidence intervals, trial by trial. Applied to data from a shuttle-box avoidance experiment with Mongolian gerbils, our approach revealed performance changes occurring at multiple temporal scales within and across training sessions which were otherwise obscured in the conventional analysis. The proper assessment of the behavioral dynamics of learning at a high temporal resolution clarified and extended current descriptions of the process of avoidance learning. It further disambiguated the interpretation of neurophysiological signal changes recorded during training in relation to learning.
  • Thumbnail Image
    Item
    Mathematical models: A research data category?
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2016) Koprucki, Thomas; Tabelow, Karsten
    Mathematical modeling and simulation (MMS) has now been established as an essential part of the scientific work in many disciplines and application areas. It is common to categorize the involved numerical data and to some extend the corresponding scientific software as research data. Both have their origin in mathematical models. In this contribution we propose a holistic approach to research data in MMS by including the mathematical models and discuss the initial requirements for a conceptual data model for this field.
  • Thumbnail Image
    Item
    hMRI - A toolbox for using quantitative MRI in neuroscience and clinical research
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2018) Balteau, Evelyne; Tabelow, Karsten; Ashburner, John; Callaghan, Martina F.; Draganski, Bogdan; Helms, Gunther; Kherif, Ferath; Leutritz, Tobias; Lutti, Antoine; Phillips, Christophe; Reimer, Enrico; Ruthotto, Lars; Seif, Maryam; Weiskopf, Nikolaus; Ziegler, Gabriel; Mohammad, Siawoosh
    Neuroscience and clinical researchers are increasingly interested in quantitative magnetic resonance imaging (qMRI) due to its sensitivity to micro-structural properties of brain tissue such as axon, myelin, iron and water concentration.We introduce the hMRI-toolbox, an easy-to-use tool openly available on GitHub, for qMRI data handling and processing, presented together with a tutorial and example dataset. This toolbox allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R? 2, proton density PD and magnetisation transfer MT saturation) that can be used for accurate delineation of subcortical brain structures and calculation of standard and novel MRI biomarkers of tissue microstructure. Embedded in the Statistical Parametric Mapping (SPM) framework, it can be readily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps, and it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences. The hMRI-toolbox is an efficient, robust and simple framework for investigating qMRI data in neuroscience and clinical research.
  • Thumbnail Image
    Item
    Structural adaptive smoothing in diffusion tensor imaging : the R package dti
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2008) Polzehl, Jörg; Tabelow, Karsten
    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
  • Thumbnail Image
    Item
    Position-orientation adaptive smoothing of diffusion weighted magnetic resonance data (POAS)
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2011) Becker, Saskia; Tabelow, Karsten; Voss, Henning U.; Anwander, Alfred; Heidemann, Robin M.; Polzehl, Jörg
    We introduce an algorithm for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both space and diffusion direction. The method, called POAS, does not refer to a specific model for the data, like the diffusion tensor or higher order models. It works by embedding the measurement space into a space with defined metric and group operations, in this case the Lie group of three-dimensional Euclidean motion SE(3). Subsequently, pairwise comparisons of the values of the diffusion weighted signal are used for adaptation. The position-orientation adaptive smoothing preserves the edges of the observed fine and anisotropic structures. The POAS-algorithm is designed to reduce noise directly in the diffusion weighted images and consequently also to reduce bias and variability of quantities derived from the data for specific models. We evaluate the algorithm on simulated and experimental data and demonstrate that it can be used to reduce the number of applied diffusion gradients and hence acquisition time while achieving similar quality of data, or to improve the quality of data acquired in a clinically feasible scan time setting.
  • Thumbnail Image
    Item
    Consistency results and confidence intervals for adaptive l1-penalized estimators of the high-dimensional sparse precision matrix
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2016) Avanesov, Valeriy; Polzehl, Jörg; Tabelow, Karsten
    In this paper we consider the adaptive '1-penalized estimators for the precision matrix in a finite-sample setting. We show consistency results and construct confidence intervals for the elements of the true precision matrix. Additionally, we analyze the bias of these confidence intervals. We apply the estimator to the estimation of functional connectivity networks in functional Magnetic Resonance data and elaborate the theoretical results in extensive simulation experiments.
  • Thumbnail Image
    Item
    Adaptive smoothing of digital images : the R package adimpro
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2006) Polzehl, Jörg; Tabelow, Karsten
    Digital imaging has become omnipresent in the past years with a bulk of applications ranging from medical imaging to photography. When pushing the limits of resolution and sensitivity noise has ever been a major issue. However, commonly used non-adaptive filters can do noise reduction at the cost of a reduced effective spatial resolution only. Here we present a new package adimpro for R, which implements the Propagation-Separation approach by Polzehl and Spokoiny (2006) for smoothing digital images. This method naturally adapts to different structures of different size in the image and thus avoids oversmoothing edges and fine structures. We extend the method for imaging data with spatial correlation. Furthermore we show how the estimation of the dependence between variance and mean value can be included. We illustrate the use of the package through some examples.
  • Thumbnail Image
    Item
    Utilizing anatomical information for signal detection in functional magnetic resonance imaging
    (Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2021) Neumann, André; Peitek, Norman; Brechmann, André; Tabelow, Karsten; Dickhaus, Thorsten
    We are considering the statistical analysis of functional magnetic resonance imaging (fMRI) data. As demonstrated in previous work, grouping voxels into regions (of interest) and carrying out a multiple test for signal detection on the basis of these regions typically leads to a higher sensitivity when compared with voxel-wise multiple testing approaches. In the case of a multi-subject study, we propose to define the regions for each subject separately based on their individual brain anatomy, represented, e.g., by so-called Aparc labels. The aggregation of the subject-specific evidence for the presence of signals in the different regions is then performed by means of a combination function for p-values. We apply the proposed methodology to real fMRI data and demonstrate that our approach can perform comparably to a two-stage approach for which two independent experiments are needed, one for defining the regions and one for actual signal detection.