Browsing by Author "Polzehl, Jörg"
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- ItemAccurate localization of brain activity in presurgical fMRI by structure adaptive smoothing(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2006) Tabelow, Karsten; Polzehl, Jörg; Uluğ, Aziz M.; Dyke, Jonathan P.; Watts, Richard; Heier, Linda A.; Voss, Henning U.An important problem of the analysis of fMRI experiments is to achieve some noise reduction of the data without blurring the shape of the activation areas. As a novel solution to this problem, the Propagation-Separation approach (PS), a structure adaptive smoothing method, has been proposed recently. PS adapts to different shapes of activation areas by generating a spatial structure corresponding to similarities and differences between time series in adjacent locations. In this paper we demonstrate how this method results in more accurate localization of brain activity. First, it is shown in numerical simulations that PS is superior over Gaussian smoothing with respect to the accurate description of the shape of activation clusters and and results in less false detections. Second, in a study of 37 presurgical planning cases we found that PS and Gaussian smoothing often yield different results, and we present examples showing aspects of the superiority of PS as applied to presurgical planning.
- ItemAdaptive smoothing of digital images : the R package adimpro(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2006) Polzehl, Jörg; Tabelow, KarstenDigital 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.
- ItemAdaptive smoothing of multi-shell diffusion-weighted magnetic resonance data by msPOAS(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2013) Becker, Saskia; Tabelow, Karsten; Mohammadi, Siawoosh; Weiskopf, Nikolaus; Polzehl, JörgIn this article we present a noise reduction method (msPOAS) for multi-shell diffusionweighted magnetic resonance data. To our knowledge, this is the first smoothing method which allows simultaneous smoothing of all q-shells. It is applied directly to the diffusion weighted data and consequently allows subsequent analysis by any model. Due to its adaptivity, the procedure avoids blurring of the inherent structures and preserves discontinuities. MsPOAS extends the recently developed positionorientation adaptive smoothing (POAS) procedure to multi-shell experiments. At the same time it considerably simplifies and accelerates the calculations. The behavior of the algorithm msPOAS is evaluated on diffusion-weighted data measured on a single shell and on multiple shells.
- ItemAnalysing fMRI experiments with the fmri package in R. version 1.0 : a user's guide(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2006) Polzehl, Jörg; Tabelow, KarstenThis document describes the usage of the R package fmri to analyse functional Magnetic Resonance Imaging (fMRI) data with structure adaptive smoothing procedures (Propagation-Separation (PS) approach) as described in [7].
- ItemBeyond the diffusion tensor model: the package dti(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2010) Polzehl, Jörg; Tabelow, KarstenDiffusion weighted imaging is a magnetic resonance based method to investigate tissue micro-structure especially in the human brain via water diffusion. Since the standard diffusion tensor model for the acquired data failes in large portion of the brain voxel more sophisticated models have bee developed. Here, we report on the package dti and how some of these models can be used with the package.
- ItemConsistency 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, KarstenIn 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.
- ItemDiffusion tensor imaging : structural adaptive smoothing(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2007) Tabelow, Karsten; Polzehl, Jörg; Spokoiny, Vladimir; Voss, Henning U.Diffusion Tensor Imaging (DTI) data is characterized by a high noise level. Thus, estimation errors of quantities like anisotropy indices or the main diffusion direction used for fiber tracking are relatively large and may significantly confound the accuracy of DTI in clinical or neuroscience applications. Besides pulse sequence optimization, noise reduction by smoothing the data can be pursued as a complementary approach to increase the accuracy of DTI. Here, we suggest an anisotropic structural adaptive smoothing procedure, which is based on the Propagation-Separation method and preserves the structures seen in DTI and their different sizes and shapes. It is applied to artificial phantom data and a brain scan. We show that this method significantly improves the quality of the estimate of the diffusion tensor and hence enables one either to reduce the number of scans or to enhance the input for subsequent analysis such as fiber tracking.
- ItemDisplacement and pressure reconstruction from magnetic resonance elastography images: Application to an in silico brain model(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2022) Galarce Marín, Felipe; Tabelow, Karsten; Polzehl, Jörg; Papanikas, Christos Panagiotis; Vavourakis, Vasileios; Lilaj, Ledia; Sack, Ingolf; Caiazzo, AlfonsoThis paper investigates a data assimilation approach for non-invasive quantification of intracranial pressure from partial displacement data, acquired through magnetic resonance elastography. Data assimilation is based on a parametrized-background data weak methodology, in which the state of the physical system tissue displacements and pressure fields is reconstructed from partially available data assuming an underlying poroelastic biomechanics model. For this purpose, a physics-informed manifold is built by sampling the space of parameters describing the tissue model close to their physiological ranges, to simulate the corresponding poroelastic problem, and compute a reduced basis. Displacements and pressure reconstruction is sought in a reduced space after solving a minimization problem that encompasses both the structure of the reduced-order model and the available measurements. The proposed pipeline is validated using synthetic data obtained after simulating the poroelastic mechanics on a physiological brain. The numerical experiments demonstrate that the framework can exhibit accurate joint reconstructions of both displacement and pressure fields. The methodology can be formulated for an arbitrary resolution of available displacement data from pertinent images. It can also inherently handle uncertainty on the physical parameters of the mechanical model by enlarging the physics-informed manifold accordingly. Moreover, the framework can be used to characterize, in silico, biomarkers for pathological conditions, by appropriately training the reduced-order model. A first application for the estimation of ventricular pressure as an indicator of abnormal intracranial pressure is shown in this contribution.
- ItemGround reaction forces and external hip joint moments predict in vivo hip contact forces during gait(Amsterdam [u.a.] : Elsevier Science, 2022) Alves, Sónia A.; Polzehl, Jörg; Brisson, Nicholas M.; Bender, Alwina; Agres, Alison N.; Damm, Philipp; Duda, Georg N.Younger patients increasingly receive total hip arthroplasty (THA) as therapy for end-stage osteoarthritis. To maintain the long-term success of THA in such patients, avoiding extremely high hip loads, i.e., in vivo hip contact force (HCF), is considered essential. However, in vivo HCFs are difficult to determine and their direct measurement is limited to instrumented joint implants. It remains unclear whether external measurements of ground reaction forces (GRFs), a non-invasive, markerless and clinic-friendly measure can estimate in vivo HCFs. Using data from eight patients with instrumented hip implants, this study determined whether GRF time series data, alone or combined with other scalar variables such as hip joint moments (HJMs) and lean muscle volume (LMV), could predict the resultant HCF (rHCF) impulse using a functional linear modeling approach. Overall, single GRF time series data did not predict in vivo rHCF impulses. However, when GRF time series data were combined with LMV of the gluteus medius or sagittal HJM using a functional linear modeling approach, the in vivo rHCF impulse could be predicted from external measures only. Accordingly, this approach can predict in vivo rHCF impulses, and thus provide patients with useful insight regarding their gait behavior to avoid hip joint overloading.
- ItemHigh resolution fMRI: overcoming the signal-to-noise problem(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2008) Tabelow, Karsten; Pi¨ech, Valentin; Polzehl, Jörg; Voss, Henning U.Increasing the spatial resolution in functional Magnetic Resonance Imaging (fMRI) inherently lowers the signal-to-noise ratio (SNR). In order to still detect functionally significant activations in high-resolution images, spatial smoothing of the data is required. However, conventional non-adaptive smoothing comes with a reduced effective resolution, foiling the benefit of the higher acquisition resolution. We show how our recently proposed structural adaptive smoothing procedure for functional MRI data can improve signal detection of high-resolution fMRI experiments regardless of the lower SNR. The procedure is evaluated on human visual and sensory-motor mapping experiments. In these applications, the higher resolution could be fully utilized and high-resolution experiments were outperforming normal resolution experiments by means of both statistical significance and information content.
- ItemHigh-resolution diffusion kurtosis imaging at 3T enabled by advanced post-processing(Lausanne : Frontiers Research Foundation, 2015) Mohammadi, Siawoosh; Tabelow, Karsten; Ruthotto, Lars; Feiweier, Thorsten; Polzehl, Jörg; Weiskopf, NikolausDiffusion Kurtosis Imaging (DKI) is more sensitive to microstructural differences and can be related to more specific micro-scale metrics (e.g., intra-axonal volume fraction) than diffusion tensor imaging (DTI), offering exceptional potential for clinical diagnosis and research into the white and gray matter. Currently DKI is acquired only at low spatial resolution (2–3 mm isotropic), because of the lower signal-to-noise ratio (SNR) and higher artifact level associated with the technically more demanding DKI. Higher spatial resolution of about 1 mm is required for the characterization of fine white matter pathways or cortical microstructure. We used restricted-field-of-view (rFoV) imaging in combination with advanced post-processing methods to enable unprecedented high-quality, high-resolution DKI (1.2 mm isotropic) on a clinical 3T scanner. Post-processing was advanced by developing a novel method for Retrospective Eddy current and Motion ArtifacT Correction in High-resolution, multi-shell diffusion data (REMATCH). Furthermore, we applied a powerful edge preserving denoising method, denoted as multi-shell orientation-position-adaptive smoothing (msPOAS). We demonstrated the feasibility of high-quality, high-resolution DKI and its potential for delineating highly myelinated fiber pathways in the motor cortex. REMATCH performs robustly even at the low SNR level of high-resolution DKI, where standard EC and motion correction failed (i.e., produced incorrectly aligned images) and thus biased the diffusion model fit. We showed that the combination of REMATCH and msPOAS increased the contrast between gray and white matter in mean kurtosis (MK) maps by about 35% and at the same time preserves the original distribution of MK values, whereas standard Gaussian smoothing strongly biases the distribution.
- ItemImage analysis and statistical inference in neuroimaging with R(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2010) Tabelow, Karsten; Clayden, Jon D.; Lafaye de Micheaux, Pierre; Polzehl, Jörg; Schmid, Volker J.; Whitcher, BrandonR is a language and environment for statistical computing and graphics. It can be considered an alternative implementation of the S language developed in the 1970s and 1980s for data analysis and graphics (Becker and Chambers, 1984; Becker et al., 1988). The R language is part of the GNU project and offers versions that compile and run on almost every major operating system currently available. We highlight several R packages built specifically for the analysis of neuroimaging data in the context of functional MRI, diffusion tensor imaging, and dynamic contrast-enhanced MRI. We review their methodology and give an overview of their capabilities for neuroimaging. In addition we summarize some of the current activities in the area of neuroimaging software development in R.
- ItemImproving 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, JörgEstimation 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.
- ItemImproving Accuracy and Temporal Resolution of Learning Curve Estimation for within- and across-Session Analysis(San Francisco, California, US : PLOS, 2016) Deliano, Matthias; Tabelow, Karsten; König, Reinhard; Polzehl, JörgEstimation of learning curves is ubiquitously based on proportions of correct responses within moving trial windows. Thereby, 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 in the analysis of single-subject data 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 an avoidance learning experiment with rodents, these methods revealed performance changes occurring at multiple time scales within and across training sessions which were otherwise obscured in the conventional analysis. Our work shows that the proper assessment of the behavioral dynamics of learning at high temporal resolution can shed new light on specific learning processes, and, thus, allows to refine existing learning concepts. It further disambiguates the interpretation of neurophysiological signal changes recorded during training in relation to learning.
- ItemLocal estimation of the noise level in MRI using structural adaptation(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2014) Tabelow, Karsten; Voss, Henning U.; Polzehl, JörgWe present a method for local estimation of the signal-dependent noise level in magnetic resonance images. The procedure uses a multi-scale approach to adaptively infer on local neighborhoods with similar data distribution. It exploits a maximum-likelihood estimator for the local noise level. The validity of the method was evaluated on repeated diffusion data of a phantom and simulated data using T1-data corrupted with artificial noise. Simulation results are compared with a recently proposed estimate. The method was applied to a high-resolution diffusion dataset to obtain improved diffusion model estimation results and to demonstrate its usefulness in methods for enhancing diffusion data.
- ItemModeling high resolution MRI: Statistical issues with low SNR(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2015) Polzehl, Jörg; Tabelow, KarstenNoise 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.
- ItemModeling the orientation distribution function by mixtures of angular central Gaussian distributions(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2010) Tabelow, Karsten; Voss, Henning U.; Polzehl, JörgIn this paper we develop a tensor mixture model for diffusion weighted imaging data using an automatic model selection criterion for the order of tensor components in a voxel. We show that the weighted orientation distribution function for this model can be expanded into a mixture of angular central Gaussian distributions. We show properties of this model in extensive simulations and in a high angular resolution experimental data set. The results suggest that the model may improve imaging of cerebral fiber tracts. We demonstrate how inference on canonical model parameters may give rise to new clinical applications.
- ItemPatch-Wise Adaptive Weights Smoothing in R(Los Angeles, Calif. : UCLA, Dept. of Statistics, 2020) Polzehl, Jörg; Papafitsoros, Kostas; Tabelow, KarstenImage reconstruction from noisy data has a long history of methodological development and is based on a variety of ideas. In this paper we introduce a new method called patch-wise adaptive smoothing, that extends the propagation-separation approach by using comparisons of local patches of image intensities to define local adaptive weighting schemes for an improved balance of reduced variability and bias in the reconstruction result. We present the implementation of the new method in an R package aws and demonstrate its properties on a number of examples in comparison with other state-of-the art image reconstruction methods. © 2020, American Statistical Association. All rights reserved.
- ItemPOAS4SPM - A toolbox for SPM to denoise diffusion MRI data(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2013) Tabelow, Karsten; Mohammadi, Siawoosh; Weiskopf, Nikolaus; Polzehl, JörgWe present an implementation of a recently developed noise reduction algorithm for dMRI data, called multi-shell position orientation adaptive smoothing (msPOAS), as a toolbox for SPM. The method intrinsically adapts to the structures of different size and shape in dMRI and hence avoids blurring typically observed in non-adaptive smoothing. We give examples for the usage of the toolbox and explain the determination of experiment-dependent parameters for an optimal performance of msPOAS.
- ItemPosition-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, JörgWe 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.