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This paper proposes SAR imaging algorithm with largest coherence based on the existing SAR imaging algorithm. The basic idea of SAR imaging algorithm in imaging processing is that output signal can have maximum signal-to-noise ratio (SNR) by using the optimal imaging parameters. Traditional imaging algorithm can acquire the best focusing effect, but would bring the decoherence phenomenon in subsequent interference process. Algorithm proposed in this paper is that SAR echo adopts consistent imaging parameters in focusing processing. Although the SNR of the output signal is reduced slightly, their coherence is ensured greatly, and finally the interferogram with high quality is obtained. In this paper, two scenes of Envisat ASAR data in Zhangbei are employed to conduct experiment for this algorithm. Compared with the interferogram from the traditional algorithm, the results show that this algorithm is more suitable for SAR interferometry (InSAR) research and application. [ABSTRACT FROM AUTHOR]

Analysis of functional magnetic resonance imaging (fMRI) data has revealed that brain regions can be grouped into functional brain networks (fBNs) or communities. A community in fMRI analysis signifies a group of brain regions coupled functionally with one another. In neuroimaging, functional connectivity (FC) measure can be utilized to quantify such functionally connected regions for disease diagnosis and hence, signifies the need of devising novel FC estimation methods. In this paper, we propose a novel method of learning FC by constraining its rank and the sum of non-zero coefficients. The underlying idea is that fBNs are sparse and can be embedded in a relatively lower dimension space. In addition, we propose to extract overlapping networks. In many instances, communities are characterized as combinations of disjoint brain regions, although recent studies indicate that brain regions may participate in more than one community. In this paper, large-scale overlapping fBNs are identified on resting state fMRI data by employing non-negative matrix factorization. Our findings support the existence of overlapping brain networks. [ABSTRACT FROM AUTHOR]

This paper describes and presents a stable and reliable set of stereo-photogrammetric normative data for global and spino-pelvic sagittal alignment, as a proven reference system for evaluating/measuring a fully unconstrained natural upright neutral standing attitude in a young healthy adult population. The methodological features described in this article will enable future studies to replicate and/or directly compare a wide range of different postural tests and/or sagittal alignment assessment procedures including the study of sagittal spine shape variations occurring during gait performance. To date, the quantitative evaluation of adult spinal deformity (ASD) has been mainly confined to the X-ray imaging approach and, more recently, to 3D X-ray reconstruction. Within the existing evaluation framework an opportunity exists for an additional approach: a quantitative evaluation procedure which is easy, accurate, relatively speedy and non-ionising, in order to monitor and track the progress of patients in the areas of both surgical and non-surgical treatment. The resources and methodology described in this paper have been proven to meet all these criteria. They have enabled full 3D posture (including 3D spine shape and sagittal alignment of the skeleton) to be consistently and successfully measured in adult volunteers. All the measurement/evaluation procedures and outcomes carried out were based entirely on the new non-ionising 3D opto-electronic stereo-photogrammetric approach described in this article. The protocol for this methodology was based on a standard set of 27 pre-selected anatomical “landmarks” on the human body, providing standard reference points for observation and measurement. A total of 124 healthy subjects were successfully assessed and, for each subject, 27 individual markers were applied to the corresponding locations on his/her body. Statistical tests to investigate gender differences were also carried out. Descriptive statistics are provided for all 15 of the spino-pelvic parameters under consideration. Results indicated significant differences between genders in five sets of parameters: Kyphosis tilt, Head tilt, Pelvic tilt, Spino-pelvic angle and T1-pelvic angle. The data also demonstrate a high degree of congruity with results obtained using the X-ray method, as evidenced by the existing literature in the field. In summary, the current study presents a new stereo-photogrammetric opto-electronic technology which can be used successfully for ASD evaluation and introduces a comprehensive set of normative data analogous to those proposed in X-ray analysis for sagittal spino-pelvic and total body alignment. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy (DR) is a disease which is widely diagnosed using (colour fundus) images. Efficiency and accuracy are critical in diagnosing DR as lack of timely intervention can lead to irreversible visual impairment. In this paper, we examine strategies for scrutinizing images which affect diagnostic performance of medical practitioners via an eye-tracking study. A total of 56 subjects with 0 to 18 years of experience participated in the study. Every subject was asked to detect DR from 40 images. The findings indicate that practitioners use mainly two types of strategies characterized by either higher dwell duration or longer track length. The main findings of the study are that higher dwell-based strategy led to higher average accuracy (> 85%) in diagnosis, irrespective of the expertise of practitioner; whereas, the average obtained accuracy with a long-track length-based strategy was dependent on the expertise of the practitioner. In the second part of the paper, we use the experimental findings to recommend a scanning strategy for fast and accurate diagnosis of DR that can be potentially used by image readers. This is derived by combining the eye-tracking gaze maps of medical experts in a novel manner based on a set of rules. This strategy requires scrutiny of images in a manner which is consistent with spatial preferences found in human perception in general and in the domain of fundus images in particular. The Levenshtein distance-based assessment of gaze patterns also establish the effectiveness of the derived scanning pattern and is thus recommended for image readers. [ABSTRACT FROM AUTHOR]

In this paper we investigate the changes in the functional connectivity intensity, and some related properties, in healthy people, across the life span and at resting state. For the explicit computation of the functional connectivity we exploit a recently proposed model, that bases not only on the correlations data provided by the acquisition equipment, but also on different parameters, such as the anatomical distances between nodes and their degrees. The leading purpose of the paper is to show that the proposed approach is able to recover the main aspects of resting state condition known from the available literature, as well as to suggest new insights, perspectives and speculations from a neurobiological point of view. Our study involves 133 subjects, both males and females of different ages, with no evidence of neurological diseases or systemic disorders. First, we show how the model applies to the sample, where the subjects are grouped into 28 different groups (14 of males and 14 of females), according to their age. This leads to the construction of two graphs (one for males and one for females), that can be realistically interpreted as representative of the neural network during the resting state. Second, following the idea that the brain network is better understood by focusing on specific nodes having a kind of centrality, we refine the two output graphs by introducing a new metric that favours the selection of nodes having higher degrees. As a third step, we extensively comment and discuss the obtained results. In particular, it is remarkable that, despite a great overlapping exists between the outcomes concerning males and females, some intriguing differences appear. This motivates a deeper local investigation, which represents the fourth part of the paper, carried out through a thorough statistical analysis. As a result, we are enabled to support that, for two special age groups, a few links contribute in differentiating the behaviour of males and females. In addition, we performed an average-based comparison between the proposed model and the traditional statistical correlation-based approach, then discussing and commenting the main outlined discrepancies. [ABSTRACT FROM AUTHOR]

Accurate estimation of motion field in respiration-correlated 4DCT images, is a precondition for the analysis of patient-specific breathing dynamics and subsequent image-supported treatment planning. However, the lung motion estimation often suffers from the sliding motion. In this paper, a novel lung motion method based on the non-rigid registration of point clouds is proposed, and the tangent-plane distance is used to represent the distance term, which describes the difference between two point clouds. Local affine transformation model is used to express the non-rigid deformation of the lung motion. The final objective function is expressed in the Frobenius norm formation, and matrix optimization scheme is carried out to find out the optimal transformation parameters that minimize the objective function. A key advantage of our proposed method is that it alleviates the requirement that the source point cloud and the reference point cloud should be in one-to-one corresponding relationship, and the requirement is difficult to be satisfied in practical application. Furthermore, the proposed method takes the sliding motion of the lung into consideration and improves the registration accuracy by reducing the constraint of the motion along the tangent direction. Non-rigid registration experiments are carried out to validate the performance of the proposed method using popi-model data. The results demonstrate that the proposed method outperforms the traditional method with about 20% accuracy increase. [ABSTRACT FROM AUTHOR]

Glioma detection and segmentation is a challenging task for radiologists and clinicians. The research reported in this paper seeks to develop a better clinical decision support algorithm for clinicians diagnosis. This paper presents a probabilistic method for detection and segmentation between abnormal tissue regions and brain tumour (tumour core and edema) portions from Magnetic Resonance Imaging (MRI). A framework is constructed to learn structure of undirected graphical models that can represent the spatial relationships among variables and apply it to glioma segmentation. Compared with the pixel of image, the superpixel is more consistent with human visual cognition and contains less redundancy, thus, the superpixels are considered as the basic unit of structure learning and glioma segmentation scheme. ℓ1-regularization techniques are applied to learn the appropriate structure for modeling graphical models. Conditional Random Fields (CRF) are used to model the spatial interactions among image superpixel regions and their measurements. A number of features including statistics features, the combined features from the local binary pattern as well as gray level run length, curve features, and fractal features were extracted from each superpixel. The features are then passed by ℓ1-regularization to ensure a robust classification. The proposed method is compared with support vector machine and Fuzzy c-means to classify each superpixel into normal and abnormal tissue. The proposed system is tested for the presence of low grade as well as high grade glioma tumors on images collected from BRATS2013, BRATS2015 data set and Henan Provincial People’s Hospital (HNPPH) data set. The experiments performed provides similarity between segmented and truth image up to 91.5% by correlation method. [ABSTRACT FROM AUTHOR]

This paper presents a region-based active contour method for the segmentation of intensity inhomogeneous images using an energy functional based on local and global fitted images. A square image fitted model is defined by using both local and global fitted differences. Moreover, local and global signed pressure force functions are introduced in the solution of the energy functional to stabilize the gradient descent flow. In the final gradient descent solution, the local fitted term helps extract regions with intensity inhomogeneity, whereas the global fitted term targets homogeneous regions. A Gaussian kernel is applied to regularize the contour at each step, which not only smoothes it but also avoids the computationally expensive re-initialization. Intensity inhomogeneous images contain undesired smooth intensity variations (bias field) that alter the results of intensity-based segmentation methods. The bias field is approximated with a Gaussian distribution and the bias of intensity inhomogeneous regions is corrected by dividing the original image by the approximated bias field. In this paper, a two-phase model is first derived and then extended to a four-phase model to segment brain magnetic resonance (MR) images into the desired regions of interest. Experimental results with both synthetic and real brain MR images are used for a quantitative and qualitative comparison with state-of-the-art active contour methods to show the advantages of the proposed segmentation technique in practical terms. [ABSTRACT FROM AUTHOR]

For ensemble learning, how to select and combine the candidate classifiers are two key issues which influence the performance of the ensemble system dramatically. Random vector functional link networks (RVFL) without direct input-to-output links is one of suitable base-classifiers for ensemble systems because of its fast learning speed, simple structure and good generalization performance. In this paper, to obtain a more compact ensemble system with improved convergence performance, an improved ensemble of RVFL based on attractive and repulsive particle swarm optimization (ARPSO) with double optimization strategy is proposed. In the proposed method, ARPSO is applied to select and combine the candidate RVFL. As for using ARPSO to select the optimal base RVFL, ARPSO considers both the convergence accuracy on the validation data and the diversity of the candidate ensemble system to build the RVFL ensembles. In the process of combining RVFL, the ensemble weights corresponding to the base RVFL are initialized by the minimum norm least-square method and then further optimized by ARPSO. Finally, a few redundant RVFL is pruned, and thus the more compact ensemble of RVFL is obtained. Moreover, in this paper, theoretical analysis and justification on how to prune the base classifiers on classification problem is presented, and a simple and practically feasible strategy for pruning redundant base classifiers on both classification and regression problems is proposed. Since the double optimization is performed on the basis of the single optimization, the ensemble of RVFL built by the proposed method outperforms that built by some single optimization methods. Experiment results on function approximation and classification problems verify that the proposed method could improve its convergence accuracy as well as reduce the complexity of the ensemble system. [ABSTRACT FROM AUTHOR]

The transport and distribution of charged molecules in polyelectrolyte solutions are of both fundamental and practical importance. A practical example, which is the specific subject addressed in the present paper, is the transport and distribution of charged species into cartilage. The charged species could be a contrast agent or a drug molecule involved in diagnosis or treatment of the widespread degenerative disease osteoarthritis, which leads to degradation of articular cartilage. Associated scientific issues include the rate of transport and the equilibrium concentrations of the charged species in the cartilage and the synovial fluid. To address these questions, we present results from magnetic resonance micro-imaging experiments on a model system of articular cartilage. The experiments yield temporally and spatially resolved data on the transport of a negatively charged contrast agent (charge = -2), used in medical examinations of cartilage, into a polyelectrolyte solution, which is designed to capture the electrostatic interactions in cartilage. Also presented is a theoretical analysis of the transport where the relevant differential equations are solved using finite element techniques as well as treated with approximate analytical expressions. In the analysis, non-ideal effects are included in the treatment of the mobile species in the system. This is made possible by using results from previous Monte Carlo simulations. The results demonstrate the importance of taking non-idealities into account when data from measurements of transport of charged solutes in a system with fixed charges from biological polyelectrolytes are analyzed. [ABSTRACT FROM AUTHOR]

Purpose: Many studies have reported that carbohydrate antigen 153 (CA153) in breast secretions (BS) can discriminate breast cancer (BC) patients from healthy individuals, indicating CA153 in BS as a potential index for BC. This meta-analysis aimed to evaluate the actual diagnostic value of CA153 in BS. Methods: Related papers were obtained from Pubmed, Embase, Scopus, Ovid, Sciverse, the Cochrane library, Chinese Biomedical literature Database (CBM), Technology of Chongqing (VIP), Wan Fang Data, and Chinese National Knowledge Infrastructure (CNKI). Pooled sensitivity, specificity, and diagnostic odds ratio (DOR) of CA153 in BS for BC diagnosis were analyzed with the random effect model. SROC and the area under the curve (AUC) were applied to assess overall diagnostic efficiency. Results: This meta-analysis included five studies with a total of 329 BC patients and 381 healthy subjects. For CA153 in BS, the summary sensitivity, specificity, and DOR to diagnose BC were 0.63 (95% confidence interval (CI): 0.57∼0.68), 0.82 (95% CI: 0.78∼0.86), and 9.18 (95% CI: 4.22∼19.95), respectively. Furthermore, the AUC of BS CA153 in the diagnosis of BC was 0.8614. Conclusions: CA153 in BS is a valuable molecular marker in diagnosing BC and should be applied in standard clinical practices of BC screening upon confirmation of our findings in a larger prospective study. [ABSTRACT FROM AUTHOR]

Compressive sensing (CS) theory asserts that we can reconstruct signals and images with only a small number of samples or measurements. Recent works exploiting the nonlocal similarity have led to better results in various CS studies. To better exploit the nonlocal similarity, in this paper, we propose a non-convex smoothed rank function based model for CS image reconstruction. We also propose an efficient alternating minimization method to solve the proposed model, which reduces a difficult and coupled problem to two tractable subproblems. Experimental results have shown that the proposed method performs better than several existing state-of-the-art CS methods for image reconstruction. [ABSTRACT FROM AUTHOR]

Content-based image retrieval (CBIR) techniques have currently gained increasing popularity in the medical field because they can use numerous and valuable archived images to support clinical decisions. In this paper, we concentrate on developing a CBIR system for retrieving brain tumors in T1-weighted contrast-enhanced MRI images. Specifically, when the user roughly outlines the tumor region of a query image, brain tumor images in the database of the same pathological type are expected to be returned. We propose a novel feature extraction framework to improve the retrieval performance. The proposed framework consists of three steps. First, we augment the tumor region and use the augmented tumor region as the region of interest to incorporate informative contextual information. Second, the augmented tumor region is split into subregions by an adaptive spatial division method based on intensity orders; within each subregion, we extract raw image patches as local features. Third, we apply the Fisher kernel framework to aggregate the local features of each subregion into a respective single vector representation and concatenate these per-subregion vector representations to obtain an image-level signature. After feature extraction, a closed-form metric learning algorithm is applied to measure the similarity between the query image and database images. Extensive experiments are conducted on a large dataset of 3604 images with three types of brain tumors, namely, meningiomas, gliomas, and pituitary tumors. The mean average precision can reach 94.68%. Experimental results demonstrate the power of the proposed algorithm against some related state-of-the-art methods on the same dataset. [ABSTRACT FROM AUTHOR]

Recently, the Coherent Point Drift (CPD) algorithm has become a very popular and efficient method for point set registration. However, this method does not take into consideration the neighborhood structure information of points to find the correspondence and requires a manual assignment of the outlier ratio. Therefore, CPD is not robust for large degrees of degradation. In this paper, an improved method is proposed to overcome the two limitations of CPD. A structure descriptor, such as shape context, is used to perform the auxiliary calculation of the correspondence, and the proportion of each GMM component is adjusted by the similarity. The outlier ratio is formulated in the EM framework so that it can be automatically calculated and optimized iteratively. The experimental results on both synthetic data and real data demonstrate that the proposed method described here is more robust to deformation, noise, occlusion, and outliers than CPD and other state-of-the-art algorithms. [ABSTRACT FROM AUTHOR]

A major tenet in theoretical neuroscience is that cognitive and behavioral processes are ultimately implemented in terms of the neural system dynamics. Accordingly, a major aim for the analysis of neurophysiological measurements should lie in the identification of the computational dynamics underlying task processing. Here we advance a state space model (SSM) based on generative piecewise-linear recurrent neural networks (PLRNN) to assess dynamics from neuroimaging data. In contrast to many other nonlinear time series models which have been proposed for reconstructing latent dynamics, our model is easily interpretable in neural terms, amenable to systematic dynamical systems analysis of the resulting set of equations, and can straightforwardly be transformed into an equivalent continuous-time dynamical system. The major contributions of this paper are the introduction of a new observation model suitable for functional magnetic resonance imaging (fMRI) coupled to the latent PLRNN, an efficient stepwise training procedure that forces the latent model to capture the ‘true’ underlying dynamics rather than just fitting (or predicting) the observations, and of an empirical measure based on the Kullback-Leibler divergence to evaluate from empirical time series how well this goal of approximating the underlying dynamics has been achieved. We validate and illustrate the power of our approach on simulated ‘ground-truth’ dynamical systems as well as on experimental fMRI time series, and demonstrate that the learnt dynamics harbors task-related nonlinear structure that a linear dynamical model fails to capture. Given that fMRI is one of the most common techniques for measuring brain activity non-invasively in human subjects, this approach may provide a novel step toward analyzing aberrant (nonlinear) dynamics for clinical assessment or neuroscientific research. [ABSTRACT FROM AUTHOR]

In order to improve the monitoring and prediction of coal and gas outburst, this paper proposes a new method for dynamic regional prediction of coal and gas outburst using microseismic (MS) monitoring. The theoretical basis of this method is presented. An index evaluation system was established and applied, based on which field tests were carried out in a coal mine. The results show that seismic monitoring with frequency and energy indexes can obtain good results for mining disturbance intensity monitoring and geological structure detection; the regional stress distribution detected by seismic wave tomography is consistent with the theoretical stress field, making its use of great significance for optimizing coal and gas outburst drilling parameters and improving overall tunneling efficiency. This approach overcomes the limitations of traditional methods in the temporal and spatial dimensions and realizes dynamic and continuous monitoring of coal and gas outburst-prone areas. [ABSTRACT FROM AUTHOR]

Alzheimer’s disease (AD) affects millions of people and is a major rising problem in health care worldwide. Recent research suggests that AD could have different subtypes, presenting differences in how the disease develops. Characterizing those subtypes could be key to deepen the understanding of this complex disease. In this paper, we used a multivariate, non-supervised clustering method over blood-based markers to find subgroups of patients defined by distinctive blood marker profiles. Our analysis on ADNI database identified 4 possible subgroups, each with a different blood profile. More importantly, we show that subgroups with different profiles have a different relationship between brain phenotypes detected in magnetic resonance imaging and disease condition. [ABSTRACT FROM AUTHOR]

Time-dependent data collected in studies of Alzheimer’s disease usually has missing and irregularly sampled data points. For this reason time series methods which assume regular sampling cannot be applied directly to the data without a pre-processing step. In this paper we use a random forest to learn the relationship between pairs of data points at different time separations. The input vector is a summary of the time series history and it includes both demographic and non-time varying variables such as genetic data. To test the method we use data from the TADPOLE grand challenge, an initiative which aims to predict the evolution of subjects at risk of Alzheimer’s disease using demographic, physical and cognitive input data. The task is to predict diagnosis, ADAS-13 score and normalised ventricles volume. While the competition proceeds, forecasting methods may be compared using a leaderboard dataset selected from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and with standard metrics for measuring accuracy. For diagnosis, we find an mAUC of 0.82, and a classification accuracy of 0.73 compared with a benchmark SVM predictor which gives mAUC = 0.62 and BCA = 0.52. The results show that the method is effective and comparable with other methods. [ABSTRACT FROM AUTHOR]

Diffusion MRI derives its contrast from MR signal attenuation induced by the movement of water molecules in microstructural environments. Associated with the signal attenuation is the reduction of signal-to-noise ratio (SNR). Methods based on total variation (TV) have shown superior performance in image noise reduction. However, TV denoising can result in stair-casing effects due to the inherent piecewise-constant assumption. In this paper, we propose a tight wavelet frame based approach for edge-preserving denoising of diffusion-weighted (DW) images. Specifically, we employ the unitary extension principle (UEP) to generate frames that are discrete analogues to differential operators of various orders, which will help avoid stair-casing effects. Instead of denoising each DW image separately, we collaboratively denoise groups of DW images acquired with adjacent gradient directions. In addition, we introduce a very efficient method for solving an ℓ0 denoising problem that involves only thresholding and solving a trivial inverse problem. We demonstrate the effectiveness of our method qualitatively and quantitatively using synthetic and real data. [ABSTRACT FROM AUTHOR]

Intravoxel incoherent motion (IVIM) imaging is a magnetic resonance imaging (MRI) technique widely used in clinical applications for various organs. However, IVIM imaging at low b-values is a persistent problem. This paper aims to investigate in a systematic and detailed manner how the number of low b-values influences the estimation of IVIM parameters. To this end, diffusion-weighted (DW) data with different low b-values were simulated to get insight into the distributions of subsequent IVIM parameters. Then, in vivo DW data with different numbers of low b-values and different number of excitations (NEX) were acquired. Finally, least-squares (LSQ) and Bayesian shrinkage prior (BSP) fitting methods were implemented to estimate IVIM parameters. The influence of the number of low b-values on IVIM parameters was analyzed in terms of relative error (RE) and structural similarity (SSIM). The results showed that the influence of the number of low b-values on IVIM parameters is variable. LSQ is more dependent on the number of low b-values than BSP, but the latter is more sensitive to noise. [ABSTRACT FROM AUTHOR]

In this paper, we present a method for automated estimation of a human face given a skull remain. Our proposed method is based on three statistical models. A volumetric (tetrahedral) skull model encoding the variations of different skulls, a surface head model encoding the head variations, and a dense statistic of facial soft tissue thickness (FSTT). All data are automatically derived from computed tomography (CT) head scans and optical face scans. In order to obtain a proper dense FSTT statistic, we register a skull model to each skull extracted from a CT scan and determine the FSTT value for each vertex of the skull model towards the associated extracted skin surface. The FSTT values at predefined landmarks from our statistic are well in agreement with data from the literature. To recover a face from a skull remain, we first fit our skull model to the given skull. Next, we generate spheres with radius of the respective FSTT value obtained from our statistic at each vertex of the registered skull. Finally, we fit a head model to the union of all spheres. The proposed automated method enables a probabilistic face-estimation that facilitates forensic recovery even from incomplete skull remains. The FSTT statistic allows the generation of plausible head variants, which can be adjusted intuitively using principal component analysis. We validate our face recovery process using an anonymized head CT scan. The estimation generated from the given skull visually compares well with the skin surface extracted from the CT scan itself. [ABSTRACT FROM AUTHOR]

We describe in this paper the experimental procedure, the data treatment and the quantification of the black body correction: an experimental approach to compensate for scattering and systematic biases in quantitative neutron imaging based on experimental data. The correction algorithm is based on two steps; estimation of the scattering component and correction using an enhanced normalization formula. The method incorporates correction terms into the image normalization procedure, which usually only includes open beam and dark current images (open beam correction). Our aim is to show its efficiency and reproducibility: we detail the data treatment procedures and quantitatively investigate the effect of the correction. Its implementation is included within the open source CT reconstruction software MuhRec. The performance of the proposed algorithm is demonstrated using simulated and experimental CT datasets acquired at the ICON and NEUTRA beamlines at the Paul Scherrer Institut. [ABSTRACT FROM AUTHOR]

Needles are commonly used in the clinic for percutaneous procedures. The outcome of such procedures heavily depends on accurate placement of the needle. There are two main challenges to achieve high accuracy: First, aligning the needle with the targeted lesion, and second, compensating for the deflection of the needle in the tissue. In order to address these challenges, scientists have developed several robotic setups for needle steering. However, the subject is still under research and reliable implementations which can be used in clinical practice are not yet available. In this paper, we have taken some steps in order to bring needle steering closer to practice. A new hybrid control algorithm is developed, which enables us to control a flexible needle by combing base-manipulation and beveled-tip steering methods. A pre-operative path planner is developed which considers the clinical requirements. The proposed method is tested in the lung of a fresh-frozen human cadaver. The work-flow of the experiments are similar to the current clinical practice. Three experimental cases are used to evaluate the proposed steering algorithm. Experimental Case I shows that using the proposed steering algorithm controllability of the needle is increased. In Case II and Case III, the needle is steered in a gelatin phantom and a human cadaver, respectively. The targeting accuracy of 1.35±0.49mm in gelatin phantom and 1.97±0.89mm in cadave is achieved. A feasibility study is performed, in which a fine needle aspiration (FNA) needle is steered in the lungs of a human cadaver under computed tomography guidance. The targeting error for the feasibility study is 2.89±0.22mm. The results suggest that such a robotic system can be beneficial for clinical use and the patient receives less x-ray radiation. [ABSTRACT FROM AUTHOR]

This paper presents a variational framework for dense diffeomorphic atlas-mapping onto high-throughput histology stacks at the 20 μm meso-scale. The observed sections are modelled as Gaussian random fields conditioned on a sequence of unknown section by section rigid motions and unknown diffeomorphic transformation of a three-dimensional atlas. To regularize over the high-dimensionality of our parameter space (which is a product space of the rigid motion dimensions and the diffeomorphism dimensions), the histology stacks are modelled as arising from a first order Sobolev space smoothness prior. We show that the joint maximum a-posteriori, penalized-likelihood estimator of our high dimensional parameter space emerges as a joint optimization interleaving rigid motion estimation for histology restacking and large deformation diffeomorphic metric mapping to atlas coordinates. We show that joint optimization in this parameter space solves the classical curvature non-identifiability of the histology stacking problem. The algorithms are demonstrated on a collection of whole-brain histological image stacks from the Mouse Brain Architecture Project. [ABSTRACT FROM AUTHOR]

Purpose: This paper lays the groundwork for linking Hounsfield unit measurements to the International System of Units (SI), ultimately enabling traceable measurements across X-ray CT (XCT) machines. We do this by characterizing a material basis that may be used in XCT reconstruction giving linear combinations of concentrations of chemical elements (in the SI units of mol/m3) which may be observed at each voxel. By implication, linear combinations not in the set are not observable. Methods and materials: We formulated a model for our material basis with a set of measurements of elemental powders at four tube voltages, 80 kV, 100 kV, 120 kV, and 140 kV, on a medical XCT. The samples included 30 small plastic bottles of powders containing various compounds spanning the atomic numbers up to 20, and a bottle of water and one of air. Using the chemical formulas and measured masses, we formed a matrix giving the number of Hounsfield units per (mole per cubic meter) at each tube voltage for each of 13 chemical elements. We defined a corresponding matrix in units we call molar Hounsfield unit (HU) potency, the difference in HU values that an added mole per cubic meter in a given voxel would add to the measured HU value. We built a matrix of molar potencies for each chemical element and tube voltage and performed a singular value decomposition (SVD) on these to formulate our material basis. We determined that the dimension of this basis is two. We then compared measurements in this material space with theoretical measurements, combining XCOM cross section data with the tungsten anode spectral model using interpolating cubic splines (TASMICS), a one-parameter filter, and a simple detector model, creating a matrix similar to our experimental matrix for the first 20 chemical elements. Finally, we compared the model predictions to Hounsfield unit measurements on three XCT calibration phantoms taken from the literature. Results: We predict the experimental HU potency values derived from our scans of chemical elements with our theoretical model built from XCOM data. The singular values and singular vectors of the model and powder measurements are in substantial agreement. Application of the Bayesian Information Criterion (BIC) shows that exactly two singular values and singular vectors describe the results over four tube voltages. We give a good account of the HU values from the literature, measured for the calibration phantoms at several tube voltages for several commercial instruments, compared with our theoretical model without introducing additional parameters. Conclusions: We have developed a two-dimensional material basis that specifies the degree to which individual elements in compounds effect the HU values in XCT images of samples with elements up to atomic number Z = 20. We show that two dimensions is sufficient given the contrast and noise in our experiment. The linear combination of concentrations of elements that can be observed using a medical XCT have been characterized, providing a material basis for use in dual-energy reconstruction. This approach provides groundwork for improved reconstruction and for the link of Hounsfield units to the SI. [ABSTRACT FROM AUTHOR]

Analytical CT reconstruction is popular in practice because of its computational efficiency, but it suffers from low reconstruction quality when an insufficient number of projections are used. To address this issue, this paper presents a new analytical method of backprojection Wiener deconvolution (BPWD). BPWD executes backprojection first, and then applies a Wiener deconvolution to the whole backprojected image. The Wiener filter is derived from a ramp filter, enabling the proposed approach to perform reconstruction and denoising simultaneously. The use of a filter after backprojection does not differentiate between real sampled projections and interpolated ones, introducing reconstruction errors. Therefore a weighted ramp filter was applied to increase the contribution of real sampled projections in the reconstruction, thus improving reconstruction quality. Experiments on synthetic data and real phase-contrast x-ray images showed that the proposed approach yields better reconstruction quality compared to the classical filtered backprojection (FBP) method, with comparable reconstruction speed. [ABSTRACT FROM AUTHOR]

This paper investigates a brain-based approach for visual merchandising display (VMD) in fashion stores. In marketing, VMD has become a research topic of interest. However, VMD research using brain activation information is rare. We examine the hemodynamic responses (HRs) in the prefrontal cortex (PFC) using functional near-infrared spectroscopy (fNIRS) while positive/negative displays of four stores (menswear, womenswear, underwear, and sportswear) are shown to 20 subjects. As features for classifying the HRs, the mean, variance, peak, skewness, kurtosis, t-value, and slope of the signals for a 20-sec time window for the activated channels are analyzed. Linear discriminant analysis is used for classifying two-class (positive and negative displays) and four-class (four fashion stores) models. PFC brain activation maps based on t-values depicting the data from the 16 channels are provided. In the two-class classification, the underwear store had the highest average classification result of 67.04%, whereas the menswear store had the lowest value of 64.15%. Men’s classification accuracy for the underwear stores with positive and negative displays was 71.38%, whereas the highest classification accuracy obtained by women for womenswear stores was 73%. The average accuracy over the 20 subjects for positive displays was 50.68%, while that of negative displays was 51.07%. Therefore, these findings suggest that human brain activation is involved in the evaluation of the fashion store displays. It is concluded that fNIRS can be used as a brain-based tool in the evaluation of fashion stores in a daily life environment. [ABSTRACT FROM AUTHOR]

Pneumonia is one of the major causes of child mortality, yet with a timely diagnosis, it is usually curable with antibiotic therapy. In many developing regions, diagnosing pneumonia remains a challenge, due to shortages of medical resources. Lung ultrasound has proved to be a useful tool to detect lung consolidation as evidence of pneumonia. However, diagnosis of pneumonia by ultrasound has limitations: it is operator-dependent, and it needs to be carried out and interpreted by trained personnel. Pattern recognition and image analysis is a potential tool to enable automatic diagnosis of pneumonia consolidation without requiring an expert analyst. This paper presents a method for automatic classification of pneumonia using ultrasound imaging of the lungs and pattern recognition. The approach presented here is based on the analysis of brightness distribution patterns present in rectangular segments (here called “characteristic vectors“) from the ultrasound digital images. In a first step we identified and eliminated the skin and subcutaneous tissue (fat and muscle) in lung ultrasound frames, and the “characteristic vectors”were analyzed using standard neural networks using artificial intelligence methods. We analyzed 60 lung ultrasound frames corresponding to 21 children under age 5 years (15 children with confirmed pneumonia by clinical examination and X-rays, and 6 children with no pulmonary disease) from a hospital based population in Lima, Peru. Lung ultrasound images were obtained using an Ultrasonix ultrasound device. A total of 1450 positive (pneumonia) and 1605 negative (normal lung) vectors were analyzed with standard neural networks, and used to create an algorithm to differentiate lung infiltrates from healthy lung. A neural network was trained using the algorithm and it was able to correctly identify pneumonia infiltrates, with 90.9% sensitivity and 100% specificity. This approach may be used to develop operator-independent computer algorithms for pneumonia diagnosis using ultrasound in young children. [ABSTRACT FROM AUTHOR]

In this paper we present a computer aided detection (CAD) system for automated measurement of the fetal head circumference (HC) in 2D ultrasound images for all trimesters of the pregnancy. The HC can be used to estimate the gestational age and monitor growth of the fetus. Automated HC assessment could be valuable in developing countries, where there is a severe shortage of trained sonographers. The CAD system consists of two steps: First, Haar-like features were computed from the ultrasound images to train a random forest classifier to locate the fetal skull. Secondly, the HC was extracted using Hough transform, dynamic programming and an ellipse fit. The CAD system was trained on 999 images and validated on an independent test set of 335 images from all trimesters. The test set was manually annotated by an experienced sonographer and a medical researcher. The reference gestational age (GA) was estimated using the crown-rump length measurement (CRL). The mean difference between the reference GA and the GA estimated by the experienced sonographer was 0.8 ± 2.6, −0.0 ± 4.6 and 1.9 ± 11.0 days for the first, second and third trimester, respectively. The mean difference between the reference GA and the GA estimated by the medical researcher was 1.6 ± 2.7, 2.0 ± 4.8 and 3.9 ± 13.7 days. The mean difference between the reference GA and the GA estimated by the CAD system was 0.6 ± 4.3, 0.4 ± 4.7 and 2.5 ± 12.4 days. The results show that the CAD system performs comparable to an experienced sonographer. The presented system shows similar or superior results compared to systems published in literature. This is the first automated system for HC assessment evaluated on a large test set which contained data of all trimesters of the pregnancy. [ABSTRACT FROM AUTHOR]

How can we predict the occurrence of acute kidney injury (AKI) in cancer patients based on machine learning with serum creatinine data? Given irregular and heterogeneous clinical data, how can we make the most of it for accurate AKI prediction? AKI is a common and significant complication in cancer patients, and correlates with substantial morbidity and mortality. Since no effective treatment for AKI still exists, it is important to take timely preventive measures. While several approaches have been proposed for predicting AKI, their scope and applicability are limited as they either assume regular data measured over a short hospital stay, or do not fully utilize heterogeneous data. In this paper, we provide an AKI prediction model with a greater applicability, which relaxes the constraints of existing approaches, and fully utilizes irregular and heterogeneous data for learning the model. In a cohort of 21,022 cancer patients who were registered into Korea Central Cancer Registry (KCCR) in Seoul National University Hospital between January 1, 2004 and December 31, 2013, our method achieves 0.7892 precision, 0.7506 recall, and 0.7576 F-measure in predicting whether a patient will develop AKI during the next 14 days. [ABSTRACT FROM AUTHOR]

As an important way to help express the preference relation between alternatives, distributed preference relation (DPR) can represent the preferred, non-preferred, indifferent, and uncertain degrees of one alternative over another simultaneously. DPR, however, is unavailable in some situations where a decision maker cannot provide the precise degrees of one alternative over another due to lack of knowledge, experience, and data. In this paper, to address this issue, we propose interval-valued DPR (IDPR) and present its properties of validity and normalization. Through constructing two optimization models, an IDPR matrix is transformed into a score matrix to facilitate the comparison between any two alternatives. The properties of the score matrix are analyzed. To guarantee the rationality of the comparisons between alternatives derived from the score matrix, the additive consistency of the score matrix is developed. In terms of these, IDPR is applied to model and solve multiple criteria group decision making (MCGDM) problem. Particularly, the relationship between the parameters for the consistency of the score matrix associated with each decision maker and those for the consistency of the score matrix associated with the group of decision makers is analyzed. A manager selection problem is investigated to demonstrate the application of IDPRs to MCGDM problems. [ABSTRACT FROM AUTHOR]

There is a current interest in quantifying time-varying connectivity (TVC) based on neuroimaging data such as fMRI. Many methods have been proposed, and are being applied, revealing new insight into the brain’s dynamics. However, given that the ground truth for TVC in the brain is unknown, many concerns remain regarding the accuracy of proposed estimates. Since there exist many TVC methods it is difficult to assess differences in time-varying connectivity between studies. In this paper, we present tvc_benchmarker, which is a Python package containing four simulations to test TVC methods. Here, we evaluate five different methods that together represent a wide spectrum of current approaches to estimating TVC (sliding window, tapered sliding window, multiplication of temporal derivatives, spatial distance and jackknife correlation). These simulations were designed to test each method’s ability to track changes in covariance over time, which is a key property in TVC analysis. We found that all tested methods correlated positively with each other, but there were large differences in the strength of the correlations between methods. To facilitate comparisons with future TVC methods, we propose that the described simulations can act as benchmark tests for evaluation of methods. Using tvc_benchmarker researchers can easily add, compare and submit their own TVC methods to evaluate its performance. [ABSTRACT FROM AUTHOR]

Background: Diffusion tensor imaging (DTI) has been suggested as a potential biomarker of disease progression, neurodegeneration and de/remyelination in MS. However, the pathological substrates that underpin alterations in brain diffusivity are not yet fully delineated. We propose that in highly cohesive fiber tracts: 1) a relative increase in parallel (axial) diffusivity (AD) may serve as a measure of increased extra-cellular space (ESC) within the core of chronic MS lesions and, as a result, may provide an estimate of the degree of tissue destruction, and 2) the contribution of the increased extra-cellular water to perpendicular (radial) diffusivity (RD) can be eliminated to provide a more accurate assessment of membranal (myelin) loss. Objective: The purpose of this study was to isolate the contribution of extra-cellular water and demyelination to observed DTI indices in the core of chronic MS lesions, using the OR as an anatomically cohesive tract. Method: Pre- and post-gadolinium (Gd) enhanced T1, T2 and DTI images were acquired from 75 consecutive RRMS patients. In addition, 25 age and gender matched normal controls were imaged using an identical MRI protocol (excluding Gd). The optic radiation (OR) was identified in individual patients using probabilistic tractography. The T2 lesions were segmented and intersected with the OR. Average eigenvalues were calculated within the core of OR lesions mask. The proportion of extra-cellular space (ECS) within the lesional core was calculated based on relative increase of AD, which was then used to normalise the perpendicular eigenvalues to eliminate the effect of the expanded ECS. In addition, modelling was implemented to simulate potential effect of various factors on lesional anisotropy. Results: Of 75 patients, 41 (55%) demonstrated sizable T2 lesion volume within the ORs. All lesional eigenvalues were significantly higher compared to NAWM and controls. There was a strong correlation between AD and RD within the core of OR lesions, which was, however, not seen in OR NAWM of MS patients or normal controls. In addition, lesional anisotropy (FA) was predominantly driven by the perpendicular diffusivity, while in NAWM and in OR of normal controls all eigenvectors contributed to variation in FA. Estimated volume of ECS component constituted significant proportion of OR lesional volume and correlated significantly with lesional T1 hypointensity. While perpendicular diffusivity dropped significantly following normalisation, it still remained higher compared with diffusivity in OR NAWM. The “residual” perpendicular diffusivity also showed a substantial reduction of inter-subject variability. Both observed and modelled diffusion data suggested anisotropic nature of water diffusion in ESC. In addition, the simulation procedure offered a possible explanation for the discrepancy in relationship between eigenvalues and anisotropy in lesional tissue and NAWM. Conclusion: This paper presents a potential technique for more reliably quantifying the effects of neurodegeneration (tissue loss) versus demyelination in OR MS lesions. This may provide a simple and effective way for applying single tract diffusion analysis in MS clinical trials, with particular relevance to pro-remyelinating and neuroprotective therapeutics. [ABSTRACT FROM AUTHOR]

Dynamic magnetic resonance imaging (DMRI) is used to noninvasively trace the movements of organs and the process of drug delivery. The results can provide quantitative or semiquantitative pathology-related parameters, thus giving DMRI great potential for clinical applications. However, conventional DMRI techniques suffer from low temporal resolution and long scan time owing to the limitations of the k-space sampling scheme and image reconstruction algorithm. In this paper, we propose a novel DMRI sampling scheme based on a golden-ratio Cartesian trajectory in combination with a compressed sensing reconstruction algorithm. The results of two simulation experiments, designed according to the two major DMRI techniques, showed that the proposed method can improve the temporal resolution and shorten the scan time and provide high-quality reconstructed images. [ABSTRACT FROM AUTHOR]

This paper presents a novel two-stage image segmentation method using an edge scaled energy functional based on local and global information for intensity inhomogeneous image segmentation. In the first stage, we integrate global intensity term with a geodesic edge term, which produces a preliminary rough segmentation result. Thereafter, by taking final contour of the first stage as initial contour, we begin second stage segmentation process by integrating local intensity term with geodesic edge term to get final segmentation result. Due to the suitable initialization from the first stage, the second stage precisely achieves desirable segmentation result for inhomogeneous image segmentation. Two stage segmentation technique not only increases the accuracy but also eliminates the problem of initial contour existed in traditional local segmentation methods. The energy function of the proposed method uses both global and local terms incorporated with compacted geodesic edge term in an additive fashion which uses image gradient information to delineate obscured boundaries of objects inside an image. A Gaussian kernel is adapted for the regularization of the level set function and to avoid an expensive re-initialization. The experiments were carried out on synthetic and real images. Quantitative validations were performed on Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) 2015 and PH2 skin lesion database. The visual and quantitative comparisons will demonstrate the efficiency of the proposed method. [ABSTRACT FROM AUTHOR]

This paper explores a new method for rapid structural damage inspection of steel tube slab (STS) structures along randomly measured paths based on a combination of compressive sampling (CS) and ultrasonic computerized tomography (UCT). In the measurement stage, using fewer randomly selected paths rather than the whole measurement net is proposed to detect the underlying damage of a concrete-filled steel tube. In the imaging stage, the ℓ1-minimization algorithm is employed to recover the information of the microstructures based on the measurement data related to the internal situation of the STS structure. A numerical concrete tube model, with the various level of damage, was studied to demonstrate the performance of the rapid UCT technique. Real-world concrete-filled steel tubes in the Shenyang Metro stations were detected using the proposed UCT technique in a CS framework. Both the numerical and experimental results show the rapid UCT technique has the capability of damage detection in an STS structure with a high level of accuracy and with fewer required measurements, which is more convenient and efficient than the traditional UCT technique. [ABSTRACT FROM AUTHOR]

Background: Putaminal diffusivity in brain magnetic resonance diffusion-weighted imaging (DWI) is increased in patients with the parkinsonian variant of multiple system atrophy (MSA-P) compared to Parkinson disease (PD) patients. Purpose: We performed a systematic review and meta-analysis to evaluate the diagnostic accuracy of DWI to distinguish MSA-P from PD. Methods: Studies on DWI were identified through a systematic PubMed and Clarivate Analytics® Web of Science® Core Collection search. Papers were selected based on stringent inclusion criteria; minimum requirement was the inclusion of MSA-P and PD patients and documented true positive, true negative, false positive and false negative rates or overall sample size and reported sensitivity and specificity. Meta-analysis was performed using the hierarchical summary receiver operating characteristics curve approach. Results: The database search yielded 1678 results of which 9 studies were deemed relevant. Diagnostic accuracy of putaminal diffusivity measurements were reported in all of these 9 studies, whereas results of other regions of interest were only reported irregularly. Therefore, a meta-analysis could only be performed for putaminal diffusivity measurements: 127 patients with MSA-P, 262 patients with PD and 70 healthy controls were included in the quantitative synthesis. The meta-analysis showed an overall sensitivity of 90% (95% confidence interval (CI): 76.7%-95.8%) and an overall specificity of 93% (95% CI: 80.0%-97.7%) to distinguish MSA-P from PD based on putaminal diffusivity. Conclusion: Putaminal diffusivity yields high sensitivity and specificity to distinguish clinically diagnosed patients with MSA-P from PD. The confidence intervals indicate substantial variability. Further multicenter studies with harmonized protocols are warranted particularly in early disease stages when clinical diagnosis is less certain. [ABSTRACT FROM AUTHOR]

Objective: Electrical Impedance Tomography (EIT) is a powerful non-invasive technique for imaging applications. The goal is to estimate the electrical properties of living tissues by measuring the potential at the boundary of the domain. Being safe with respect to patient health, non-invasive, and having no known hazards, EIT is an attractive and promising technology. However, it suffers from a particular technical difficulty, which consists of solving a nonlinear inverse problem in real time. Several nonlinear approaches have been proposed as a replacement for the linear solver, but in practice very few are capable of stable, high-quality, and real-time EIT imaging because of their very low robustness to errors and inaccurate modeling, or because they require considerable computational effort. Methods: In this paper, a post-processing technique based on an artificial neural network (ANN) is proposed to obtain a nonlinear solution to the inverse problem, starting from a linear solution. While common reconstruction methods based on ANNs estimate the solution directly from the measured data, the method proposed here enhances the solution obtained from a linear solver. Conclusion: Applying a linear reconstruction algorithm before applying an ANN reduces the effects of noise and modeling errors. Hence, this approach significantly reduces the error associated with solving 2D inverse problems using machine-learning-based algorithms. Significance: This work presents radical enhancements in the stability of nonlinear methods for biomedical EIT applications. [ABSTRACT FROM AUTHOR]

Stationary digital breast tomosynthesis (sDBT) with distributed X-ray sources based on carbon nanotube (CNT) field emission cathodes has been recently proposed as an approach that can prevent motion blur produced by traditional DBT systems. In this paper, we simulate a geometric calibration method based on a proposed multi-source CNT X-ray sDBT system. This method is a projection matrix-based approach with seven geometric parameters, all of which can be obtained from only one projection datum of the phantom. To our knowledge, this study reports the first application of this approach in a CNT-based multi-beam X-ray sDBT system. The simulation results showed that the extracted geometric parameters from the calculated projection matrix are extremely close to the input values and that the proposed method is effective and reliable for a square sDBT system. In addition, a traditional cone-beam computed tomography (CT) system was also simulated, and the uncalibrated and calibrated geometric parameters were used in image reconstruction based on the filtered back-projection (FBP) method. The results indicated that the images reconstructed with calibrated geometric parameters have fewer artifacts and are closer to the reference image. All the simulation tests showed that this geometric calibration method is optimized for sDBT systems but can also be applied to other application-specific CT imaging systems. [ABSTRACT FROM AUTHOR]

This paper introduces a new framework for the segmentation of different brain structures (white matter, gray matter, and cerebrospinal fluid) from 3D MR brain images at different life stages. The proposed segmentation framework is based on a shape prior built using a subset of co-aligned training images that is adapted during the segmentation process based on first- and second-order visual appearance characteristics of MR images. These characteristics are described using voxel-wise image intensities and their spatial interaction features. To more accurately model the empirical grey level distribution of the brain signals, we use a linear combination of discrete Gaussians (LCDG) model having positive and negative components. To accurately account for the large inhomogeneity in infant MRIs, a higher-order Markov-Gibbs Random Field (MGRF) spatial interaction model that integrates third- and fourth- order families with a traditional second-order model is proposed. The proposed approach was tested and evaluated on 102 3D MR brain scans using three metrics: the Dice coefficient, the 95-percentile modified Hausdorff distance, and the absolute brain volume difference. Experimental results show better segmentation of MR brain images compared to current open source segmentation tools. [ABSTRACT FROM AUTHOR]

In this paper we evaluate the three main methods for correcting the susceptibility-induced artefact in diffusion-weighted magnetic-resonance (DW-MR) data, and assess how correction is affected by the susceptibility field’s interaction with motion. The susceptibility artefact adversely impacts analysis performed on the data and is typically corrected in post-processing. Correction strategies involve either registration to a structural image, the application of an acquired field-map or the use of additional images acquired with different phase-encoding. Unfortunately, the choice of which method to use is made difficult by the absence of any systematic comparisons of them. In this work we quantitatively evaluate these methods, by extending and employing a recently proposed framework that allows for the simulation of realistic DW-MR datasets with artefacts. Our analysis separately evaluates the ability for methods to correct for geometric distortions and to recover lost information in regions of signal compression. In terms of geometric distortions, we find that registration-based methods offer the poorest correction. Field-mapping techniques are better, but are influenced by noise and partial volume effects, whilst multiple phase-encode methods performed best. We use our simulations to validate a popular surrogate metric of correction quality, the comparison of corrected data acquired with AP and LR phase-encoding, and apply this surrogate to real datasets. Furthermore, we demonstrate that failing to account for the interaction of the susceptibility field with head movement leads to increased errors when analysing DW-MR data. None of the commonly used post-processing methods account for this interaction, and we suggest this may be a valuable area for future methods development. [ABSTRACT FROM AUTHOR]

Statistical Parametric Mapping (SPM) is the dominant paradigm for mass-univariate analysis of neuroimaging data. More recently, a Bayesian approach termed Posterior Probability Mapping (PPM) has been proposed as an alternative. PPM offers two advantages: (i) inferences can be made about effect size thus lending a precise physiological meaning to activated regions, (ii) regions can be declared inactive. This latter facility is most parsimoniously provided by PPMs based on Bayesian model comparisons. To date these comparisons have been implemented by an Independent Model Optimization (IMO) procedure which separately fits null and alternative models. This paper proposes a more computationally efficient procedure based on Savage-Dickey approximations to the Bayes factor, and Taylor-series approximations to the voxel-wise posterior covariance matrices. Simulations show the accuracy of this Savage-Dickey-Taylor (SDT) method to be comparable to that of IMO. Results on fMRI data show excellent agreement between SDT and IMO for second-level models, and reasonable agreement for first-level models. This Savage-Dickey test is a Bayesian analogue of the classical SPM-F and allows users to implement model comparison in a truly interactive manner. [ABSTRACT FROM AUTHOR]

Accurate and robust tomographic reconstruction from dynamic positron emission tomography (PET) acquired data is a difficult problem. Conventional methods, such as the maximum likelihood expectation maximization (MLEM) algorithm for reconstructing the activity distribution-based on individual frames, may lead to inaccurate results due to the checkerboard effect and limitation of photon counts. In this paper, we propose a stacked sparse auto-encoder based reconstruction framework for dynamic PET imaging. The dynamic reconstruction problem is formulated in a deep learning representation, where the encoding layers extract the prototype features, such as edges, so that, in the decoding layers, the reconstructed results are obtained through a combination of those features. The qualitative and quantitative results of the procedure, including the data based on a Monte Carlo simulation and real patient data demonstrates the effectiveness of our method. [ABSTRACT FROM AUTHOR]

It is often a difficult task to accurately segment brain magnetic resonance (MR) images with intensity in-homogeneity and noise. This paper introduces a novel level set method for simultaneous brain MR image segmentation and intensity inhomogeneity correction. To reduce the effect of noise, novel anisotropic spatial information, which can preserve more details of edges and corners, is proposed by incorporating the inner relationships among the neighbor pixels. Then the proposed energy function uses the multivariate Student's t-distribution to fit the distribution of the intensities of each tissue. Furthermore, the proposed model utilizes Hidden Markov random fields to model the spatial correlation between neigh-boring pixels/voxels. The means of the multivariate Student's t-distribution can be adaptively estimated by multiplying a bias field to reduce the effect of intensity inhomogeneity. In the end, we reconstructed the energy function to be convex and calculated it by using the Split Bregman method, which allows our framework for random initialization, thereby allowing fully automated applications. Our method can obtain the final result in less than 1 second for 2D image with size 256 × 256 and less than 300 seconds for 3D image with size 256 × 256 × 171. The proposed method was compared to other state-of-the-art segmentation methods using both synthetic and clinical brain MR images and increased the accuracies of the results more than 3%. [ABSTRACT FROM AUTHOR]

Purpose: Lymphedema, a swelling of the extremity, is a debilitating morbidity of cancer treatment. Current clinical evaluation of lymphedema is often based on medical history and physical examinations, which is subjective. In this paper, the authors report an objective, quantitative 2D strain imaging approach using a hybrid deformable registration to measure soft-tissue stiffness and assess the severity of lymphedema. Methods: The authors have developed a new 2D strain imaging method using registration of pre- and post-compression ultrasound B-mode images, which combines the statistical intensity- and structure-based similarity measures using normalized mutual information (NMI) metric and normalized sum-of-squared-differences (NSSD), with an affine-based global and B-spline-based local transformation model. This 2D strain method was tested through a series of experiments using elastography phantom under various pressures. Clinical feasibility was tested with four participants: two patients with arm lymphedema following breast-cancer radiotherapy and two healthy volunteers. Results: The phantom experiments have shown that the proposed registration-based strain method significantly increased the signal-to-noise and contrast-to-noise ratio under various pressures as compared with the commonly used cross-correlation-based elastography method. In the pilot study, the strain images were successfully generated for all participants. The averaged strain values of the lymphedema affected arms were much higher than those of the normal arms. Conclusions: The authors have developed a deformable registration-based 2D strain method for the evaluation of arm lymphedema. The initial findings are encouraging and a large clinical study is warranted to further evaluate this 2D ultrasound strain imaging technology. [ABSTRACT FROM AUTHOR]

Kalman filtering methods have long been regarded as efficient adaptive Bayesian techniques for estimating hidden states in models of linear dynamical systems under Gaussian uncertainty. Recent advents of the Cubature Kalman filter (CKF) have extended this efficient estimation property to nonlinear systems, and also to hybrid nonlinear problems where by the processes are continuous and the observations are discrete (continuous-discrete CD-CKF). Employing CKF techniques, therefore, carries high promise for modeling many biological phenomena where the underlying processes exhibit inherently nonlinear, continuous, and noisy dynamics and the associated measurements are uncertain and time-sampled. This paper investigates the performance of cubature filtering (CKF and CD-CKF) in two flagship problems arising in the field of neuroscience upon relating brain functionality to aggregate neurophysiological recordings: (i) estimation of the firing dynamics and the neural circuit model parameters from electric potentials (EP) observations, and (ii) estimation of the hemodynamic model parameters and the underlying neural drive from BOLD (fMRI) signals. First, in simulated neural circuit models, estimation accuracy was investigated under varying levels of observation noise (SNR), process noise structures, and observation sampling intervals (dt). When compared to the CKF, the CD-CKF consistently exhibited better accuracy for a given SNR, sharp accuracy increase with higher SNR, and persistent error reduction with smaller dt. Remarkably, CD-CKF accuracy shows only a mild deterioration for non-Gaussian process noise, specifically with Poisson noise, a commonly assumed form of background fluctuations in neuronal systems. Second, in simulated hemodynamic models, parametric estimates were consistently improved under CD-CKF. Critically, time-localization of the underlying neural drive, a determinant factor in fMRI-based functional connectivity studies, was significantly more accurate under CD-CKF. In conclusion, and with the CKF recently benchmarked against other advanced Bayesian techniques, the CD-CKF framework could provide significant gains in robustness and accuracy when estimating a variety of biological phenomena models where the underlying process dynamics unfold at time scales faster than those seen in collected measurements. [ABSTRACT FROM AUTHOR]

The availability of digital X-ray detectors, together with advances in reconstruction algorithms, creates an opportunity for bringing 3D capabilities to conventional radiology systems. The downside is that reconstruction algorithms for non-standard acquisition protocols are generally based on iterative approaches that involve a high computational burden. The development of new flexible X-ray systems could benefit from computer simulations, which may enable performance to be checked before expensive real systems are implemented. The development of simulation/reconstruction algorithms in this context poses three main difficulties. First, the algorithms deal with large data volumes and are computationally expensive, thus leading to the need for hardware and software optimizations. Second, these optimizations are limited by the high flexibility required to explore new scanning geometries, including fully configurable positioning of source and detector elements. And third, the evolution of the various hardware setups increases the effort required for maintaining and adapting the implementations to current and future programming models. Previous works lack support for completely flexible geometries and/or compatibility with multiple programming models and platforms. In this paper, we present FUX-Sim, a novel X-ray simulation/reconstruction framework that was designed to be flexible and fast. Optimized implementation for different families of GPUs (CUDA and OpenCL) and multi-core CPUs was achieved thanks to a modularized approach based on a layered architecture and parallel implementation of the algorithms for both architectures. A detailed performance evaluation demonstrates that for different system configurations and hardware platforms, FUX-Sim maximizes performance with the CUDA programming model (5 times faster than other state-of-the-art implementations). Furthermore, the CPU and OpenCL programming models allow FUX-Sim to be executed over a wide range of hardware platforms. [ABSTRACT FROM AUTHOR]

This paper proposes a mathematical framework for understanding how the structural changes in the COPD lung reflect in model parameters. The core of the analysis is a correlation between the heterogeneity in the lung as COPD degree changes (GOLD II, III and IV) and the nonlinearity index evaluated using the forced oscillation technique. A low frequency evaluation of respiratory impedance models and nonlinearity degree is performed since changes in tissue mechanics are related to viscoelastic properties. Simulation analysis of our model indicates a good correlation to expected changes in heterogeneity and nonlinear effects. A total of 43 COPD diagnosed patients are evaluated, distributed as GOLD II (18), GOLD III (15) and GOLD IV (10). Experimental data supports the claims and indicate that the proposed model and index for nonlinearity is well-suited to capture COPD structural changes. [ABSTRACT FROM AUTHOR]