125 results match your criteria deconvolution median


Effect of adjustment for case misclassification and infection date uncertainty on estimates of COVID-19 effective reproduction number.

Epidemiology 2021 Jul 19. Epub 2021 Jul 19.

Drexel University Dornsife School of Public Health, Department of Epidemiology and Biostatistics, Philadelphia, PA, USA Drexel University Dornsife School of Public Health, Department of Environmental and Occupational Health, Philadelphia, PA, USA.

Background: Surveillance data captured during the COVID-19 pandemic may not be optimal to inform a public health response, because it is biased by imperfect test accuracy, differential access to testing, and uncertainty in date of infection.

Methods: We downloaded COVID-19 time series surveillance data from the Colorado Department of Public Health & Environment by report and illness onset dates for 9-Mar-2020 to 30-Sep-2020. We used existing Bayesian methods to first adjust for misclassification in testing and surveillance, followed by deconvolution of date of infection. Read More

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Sparse Deconvolution of Pulsatile Growth Hormone Secretion in Adolescents.

IEEE/ACM Trans Comput Biol Bioinform 2021 Jun 10;PP. Epub 2021 Jun 10.

Growth hormone (GH) is secreted by cells in the anterior pituitary on two time scales: discrete pulses over minutes that occur within a 24-hr pattern. Secretion reflects the balance of stimulatory and inhibitory inputs from the hypothalamus and is influenced by gonadal steroids, stress, nutrition, and sleep/wake states. We propose a novel approach for the analysis of GH data and use this approach to quantify (i) the timing, amplitude and the number of GH pulses and (ii) GH infusion, clearance and basal secretion (i. Read More

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Validating pore size estimates in a complex microfiber environment on a human MRI system.

Magn Reson Med 2021 09 7;86(3):1514-1530. Epub 2021 May 7.

Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, United Kingdom.

Purpose: Recent advances in diffusion-weighted MRI provide "restricted diffusion signal fraction" and restricting pore size estimates. Materials based on co-electrospun oriented hollow cylinders have been introduced to provide validation for such methods. This study extends this work, exploring accuracy and repeatability using an extended acquisition on a 300 mT/m gradient human MRI scanner, in substrates closely mimicking tissue, that is, non-circular cross-sections, intra-voxel fiber crossing, intra-voxel distributions of pore-sizes, and smaller pore-sizes overall. Read More

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September 2021

Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology.

Elife 2021 03 23;10. Epub 2021 Mar 23.

Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.

We developed genetic-epigenetic tissue mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues. We validated this approach by showing that, in pregnant women, circulating DNA carrying fetal-specific alleles was entirely placenta-derived. In lung transplant recipients, we showed that, at 72 hr after transplantation, the lung contributed only a median of 17% to the plasma DNA carrying donor-specific alleles, and hematopoietic cells contributed a median of 78%. Read More

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From Neurosurgical Planning to Histopathological Brain Tumor Characterization: Potentialities of Arcuate Fasciculus Along-Tract Diffusion Tensor Imaging Tractography Measures.

Front Neurol 2021 26;12:633209. Epub 2021 Feb 26.

Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.

Tractography has been widely adopted to improve brain gliomas' surgical planning and guide their resection. This study aimed to evaluate state-of-the-art of arcuate fasciculus (AF) tractography for surgical planning and explore the role of along-tract analyses for characterizing tumor histopathology. High angular resolution diffusion imaging (HARDI) images were acquired for nine patients with tumors located in or near language areas (age: 41 ± 14 years, mean ± standard deviation; five males) and 32 healthy volunteers (age: 39 ± 16 years; 16 males). Read More

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February 2021

Diffusion magnetic resonance imaging assessment of regional white matter maturation in preterm neonates.

Neuroradiology 2021 Apr 29;63(4):573-583. Epub 2020 Oct 29.

Centre for the Developing Brain, School of Imaging Sciences & Biomedical Engineering, King's College London, London, UK.

Purpose: Diffusion magnetic resonance imaging (dMRI) studies report altered white matter (WM) development in preterm infants. Neurite orientation dispersion and density imaging (NODDI) metrics provide more realistic estimations of neurite architecture in vivo compared with standard diffusion tensor imaging (DTI) metrics. This study investigated microstructural maturation of WM in preterm neonates scanned between 25 and 45 weeks postmenstrual age (PMA) with normal neurodevelopmental outcomes at 2 years using DTI and NODDI metrics. Read More

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The association of liver function biomarkers with internal exposure of short- and medium-chain chlorinated paraffins in residents from Jinan, China.

Environ Pollut 2021 Jan 1;268(Pt A):115762. Epub 2020 Oct 1.

Environmental Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, China. Electronic address:

Chlorinated paraffins (CPs) are pervasive environmental pollutants which have been reported to be hepatotoxic by laboratory cell and animal studies. However, the related epidemiological reports on their hepatotoxic effects to humans are sparse. In this study, we evaluated the associations between six liver enzymes and serum short-chain CP (SCCP) or medium-chain CP (MCCP) concentrations of 197 residents in Jinan, China. Read More

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January 2021

A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures.

Forensic Sci Int Genet 2020 11 11;49:102367. Epub 2020 Aug 11.

The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC, 20007, United States. Electronic address:

Microhaplotypes are emerging biomarkers for forensic applications. In this study, a sequence-based multiplex assay of 74 microhaplotypes (230 SNPs) was developed on the Ion Torrent S5™ (Thermo Fisher Scientific) system and the potential for its application to mixture deconvolution was explored. The 74 loci are distributed across the autosomal human genome and have A (i. Read More

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November 2020

Dynamic CT Myocardial Perfusion Imaging in Patients without Obstructive Coronary Artery Disease: Quantification of Myocardial Blood Flow according to Varied Heart Rate Increments after Stress.

Korean J Radiol 2021 01 11;22(1):97-105. Epub 2020 Aug 11.

Institute of Diagnostic and Interventional Radiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.

Objective: The present study aimed to investigate the association between myocardial blood flow (MBF) quantified by dynamic CT myocardial perfusion imaging (CT-MPI) and the increments in heart rate (HR) after stress in patients without obstructive coronary artery disease.

Materials And Methods: We retrospectively included 204 subjects who underwent both dynamic CT-MPI and coronary CT angiography (CCTA). Patients with more than minimal coronary stenosis (diameter ≥ 25%), history of myocardial infarction/revascularization, cardiomyopathy, and microvascular dysfunction were excluded. Read More

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January 2021

A deep learning model to predict dose-volume histograms of organs at risk in radiotherapy treatment plans.

Med Phys 2020 Nov 15;47(11):5467-5481. Epub 2020 Oct 15.

National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuannanli, Chaoyang District, Beijing, 100021, China.

Purpose: To develop a deep learning-based model to predict achievable dose-volume histograms (DVHs) of organs at risk (OARs) for automation of inverse planning.

Methods: The model was based on a connected residual deconvolution network (CResDevNet) and compared with UNet as a baseline. The DVHs of OARs are dependent on patient anatomical features of the planning target volumes and OARs, and these spatial relationships can be learned automatically from prior high-quality plans. Read More

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November 2020

Estimation of incubation period and generation time based on observed length-biased epidemic cohort with censoring for COVID-19 outbreak in China.

Biometrics 2020 Jul 6. Epub 2020 Jul 6.

Beijing International Center for Mathematical Research, Peking University, Beijing, China.

The incubation period and generation time are key characteristics in the analysis of infectious diseases. The commonly used contact-tracing-based estimation of incubation distribution is highly influenced by the individuals' judgment on the possible date of exposure, and might lead to significant errors. On the other hand, interval censoring-based methods are able to utilize a much larger set of traveling data but may encounter biased sampling problems. Read More

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Accurate stacked-sheet counting method based on deep learning.

J Opt Soc Am A Opt Image Sci Vis 2020 Jul;37(7):1206-1218

The accurate counting of laminated sheets, such as packing or printing sheets in industry, is extremely important because it greatly affects the economic cost. However, the different thicknesses, adhesion properties, and breakage points and the low contrast of sheets remain challenges to traditional counting methods based on image processing. This paper proposes a new stacked-sheet counting method with a deep learning approach using the U-Net architecture. Read More

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Accelerated Wideband Myocardial Perfusion Pulse Sequence with Compressed Sensing Reconstruction for Myocardial Blood Flow Quantification in Patients with a Cardiac Implantable Electronic Device.

Radiol Cardiothorac Imaging 2020 Apr 16;2(2):e190114. Epub 2020 Apr 16.

Department of Radiology (K.P.H., L.F., D.K.) and Division of Cardiology, Department of Internal Medicine (B.H.F., D.C.L.), Northwestern University Feinberg School of Medicine, 737 N Michigan Ave, Suite 1600, Chicago, IL 60611; Department of Radiology, Mayo Clinic, Rochester, Minn (J.D.C.); Laboratory for Advanced Cardiovascular Imaging, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Md (A.E.A., L.Y.H.); and Department of Biomedical Engineering, Northwestern University, Evanston, Ill (L.F., D.K.).

Purpose: To develop an accelerated wideband cardiac perfusion pulse sequence and test whether it can produce diagnostically acceptable image quality and whether it can be used to reliably quantify myocardial blood flow (MBF) in patients with a cardiac implantable electronic device (CIED).

Materials And Methods: A fivefold-accelerated wideband perfusion pulse sequence was developed using compressed sensing to sample one arterial input function plane and three myocardial perfusion (MP) planes per heartbeat in patients with a CIED with heart rates as high as 102 beats per minute. Resting perfusion scans were performed in 10 patients with a CIED and in 10 patients with no device as a control group. Read More

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Impact of b-value on estimates of apparent fibre density.

Hum Brain Mapp 2020 07 26;41(10):2583-2595. Epub 2020 Mar 26.

Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Wales, UK.

Recent advances in diffusion magnetic resonance imaging (dMRI) analysis techniques have improved our understanding of fibre-specific variations in white matter microstructure. Increasingly, studies are adopting multi-shell dMRI acquisitions to improve the robustness of dMRI-based inferences. However, the impact of b-value choice on the estimation of dMRI measures such as apparent fibre density (AFD) derived from spherical deconvolution is not known. Read More

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Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.

Cancer Res 2020 04 10;80(7):1512-1523. Epub 2020 Feb 10.

Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.

Darwinian evolution of tumor cells remains underexplored in childhood cancer. We here reconstruct the evolutionary histories of 56 pediatric primary tumors, including 24 neuroblastomas, 24 Wilms tumors, and 8 rhabdomyosarcomas. Whole-genome copy-number and whole-exome mutational profiling of multiple regions per tumor were performed, followed by clonal deconvolution to reconstruct a phylogenetic tree for each tumor. Read More

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Tumour heterogeneity revealed by unsupervised decomposition of dynamic contrast-enhanced magnetic resonance imaging is associated with underlying gene expression patterns and poor survival in breast cancer patients.

Breast Cancer Res 2019 10 17;21(1):112. Epub 2019 Oct 17.

Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Xiasha High Education Zone, Hangzhou, 310018, Zhejiang, China.

Background: Heterogeneity is a common finding within tumours. We evaluated the imaging features of tumours based on the decomposition of tumoural dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data to identify their prognostic value for breast cancer survival and to explore their biological importance.

Methods: Imaging features (n = 14), such as texture, histogram distribution and morphological features, were extracted to determine their associations with recurrence-free survival (RFS) in patients in the training cohort (n = 61) from The Cancer Imaging Archive (TCIA). Read More

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October 2019

Neural Network-derived Perfusion Maps for the Assessment of Lesions in Patients with Acute Ischemic Stroke.

Radiol Artif Intell 2019 Sep 11;1(5):e190019. Epub 2019 Sep 11.

Support Center for Advanced Neuroimaging-University Institute of Diagnostic and Interventional Neuroradiology (R. Meier, P.L., J.G., R.W., R. McKinley, J.K.), Department of Neurology (S.J., U.F., J.K.), Institute for Surgical Technology and Biomechanics (M.R.), and Institute for Diagnostic, Interventional and Pediatric Radiology (J.K.), University Hospital Inselspital and University of Bern, Freiburgstrasse 4, 3010 Bern, Switzerland.

Purpose: To perform a proof-of-concept study to investigate the clinical utility of perfusion maps derived from convolutional neural networks (CNNs) for the workup of patients with acute ischemic stroke presenting with a large vessel occlusion.

Materials And Methods: Data on endovascularly treated patients with acute ischemic stroke ( = 151; median age, 68 years [interquartile range, 59-75 years]; 82 of 151 [54.3%] women) were retrospectively extracted from a single-center institutional prospective registry (between January 2011 and December 2015). Read More

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September 2019

Exploring Reperfusion Following Endovascular Thrombectomy.

Stroke 2019 09 1;50(9):2389-2395. Epub 2019 Aug 1.

From the Division of Neurology (J.C.K, B.B., R.W., N.A.L., K.B.), University of Alberta, Edmonton, Canada.

Background and Purpose- Cerebral perfusion in acute ischemic stroke patients is often assessed before endovascular thrombectomy (EVT), but rarely after. Perfusion data obtained following EVT may provide additional prognostic information. We developed a tool to quantitatively derive perfusion measurements from digital subtraction angiography (DSA) data and examined perfusion in patients following EVT. Read More

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September 2019

Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry Imaging of Human Hair to Characterize Longitudinal Profiles of the Antiretroviral Maraviroc for Adherence Monitoring.

Anal Chem 2019 08 6;91(16):10816-10822. Epub 2019 Aug 6.

Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States.

Here, we assess infrared matrix assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging (MSI) analysis of hair as a clinical tool for monitoring patient adherence to the antiretroviral maraviroc (MVC). A custom MATLAB-based algorithm has been developed to streamline data analysis and generate longitudinal profiles of drug incorporation along the length of hair strands. Hair strands from volunteers enrolled in a directly observed therapy study were analyzed by IR-MALDESI MSI and processed using this tool to characterize the profiles of single doses and a daily dose regimen of MVC. Read More

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Deep learning reveals untapped information for local white-matter fiber reconstruction in diffusion-weighted MRI.

Magn Reson Imaging 2019 10 16;62:220-227. Epub 2019 Jul 16.

Computer Science, Vanderbilt University, Nashville, TN, USA; Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Electrical Engineering, Vanderbilt University, Nashville, TN, USA.

Purpose: Diffusion-weighted magnetic resonance imaging (DW-MRI) is of critical importance for characterizing in-vivo white matter. Models relating microarchitecture to observed DW-MRI signals as a function of diffusion sensitization are the lens through which DW-MRI data are interpreted. Numerous modern approaches offer opportunities to assess more complex intra-voxel structures. Read More

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October 2019

Deep semantic lung segmentation for tracking potential pulmonary perfusion biomarkers in chronic obstructive pulmonary disease (COPD): The multi-ethnic study of atherosclerosis COPD study.

J Magn Reson Imaging 2020 02 5;51(2):571-579. Epub 2019 Jul 5.

Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany.

Background: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity and mortality. Identification of imaging biomarkers for phenotyping is necessary for future treatment and therapy monitoring. However, translation of visual analytic pipelines into clinics or their use in large-scale studies is significantly slowed by time-consuming postprocessing steps. Read More

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February 2020

Fast learning of fiber orientation distribution function for MR tractography using convolutional neural network.

Med Phys 2019 Jul 11;46(7):3101-3116. Epub 2019 May 11.

Center for Brain Imaging Science and Technology, Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Hangzhou, Zhejiang, China.

Purpose: In diffusion-weighted magnetic resonance imaging (DW-MRI), the fiber orientation distribution function (fODF) is of great importance for solving complex fiber configurations to achieve reliable tractography throughout the brain, which ultimately facilitates the understanding of brain connectivity and exploration of neurological dysfunction. Recently, multi-shell multi-tissue constrained spherical deconvolution (MSMT-CSD) method has been explored for reconstructing full fODFs. To achieve a reliable fitting, similar to other model-based approaches, a large number of diffusion measurements is typically required for MSMT-CSD method. Read More

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Comparison of Intravoxel incoherent motion imaging and multiecho dynamic contrast-based MRI in rectal cancer.

J Magn Reson Imaging 2019 10 4;50(4):1114-1124. Epub 2019 Apr 4.

Department of Physics, University of Oslo, Oslo, Norway.

Background: Dynamic contrast-based MRI and intravoxel incoherent motion imaging (IVIM) MRI are both methods showing promise as diagnostic and prognostic tools in rectal cancer. Both methods aim at measuring perfusion-related parameters, but the relationship between them is unclear.

Purpose: To investigate the relationship between perfusion- and permeability-related parameters obtained by IVIM-MRI, T -weighted dynamic contrast-enhanced (DCE)-MRI and T *-weighted dynamic susceptibility contrast (DSC)-MRI. Read More

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October 2019

Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato.

Genetics 2019 05 18;212(1):317-332. Epub 2019 Mar 18.

Department of Horticulture, University of Wisconsin-Madison, Wisconsin 53706

Deconvolution of the genetic architecture underlying yield is critical for understanding bases of genetic gain in species of agronomic importance. To dissect the genetic components of yield in potato, we adopted a reference-based recombination map composed of four segregating alleles from an interspecific pseudotestcross F potato population ( = 90). Approximately 1. Read More

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Hepatic blood flow by perfusion computed tomography as an imaging biomarker for patients with gastric cancer.

Oncol Lett 2019 Mar 25;17(3):3267-3276. Epub 2019 Jan 25.

Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan.

Perfusion computed tomography (PCT) is a less invasive imaging modality that provides information about tissue hemodynamics at the capillary level. The present study aimed to investigate the correlation between hepatic perfusion and gastric cancer progression. A total of 136 patients with gastric adenocarcinoma were evaluated in the present study. Read More

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Partial-volume correction in dynamic PET-CT: effect on tumor kinetic parameter estimation and validation of simplified metrics.

EJNMMI Res 2019 Feb 4;9(1):12. Epub 2019 Feb 4.

Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.

Background: Partial-volume effects generally result in an underestimation of tumor tracer uptake on PET-CT for small lesions, necessitating partial-volume correction (PVC) for accurate quantification. However, investigation of PVC in dynamic oncological PET studies to date is scarce. The aim of this study was to investigate PVC's impact on tumor kinetic parameter estimation from dynamic PET-CT acquisitions and subsequent validation of simplified semi-quantitative metrics. Read More

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February 2019

Estimation of Ischemic Core Volume Using Computed Tomographic Perfusion.

Stroke 2018 10;49(10):2345-2352

From the Department of Radiology (Y.S., B.N.D., A.H.D., K.N.), Icahn School of Medicine at Mount Sinai, New York City, NY.

Background and Purpose- Estimation of infarction based on computed tomographic perfusion (CTP) has been challenging, mainly because of noise associated with CTP data. The Bayesian method is a robust probabilistic method that minimizes effects of oscillation, tracer delay, and noise during residue function estimation compared with other deconvolution methods. This study compares CTP-estimated ischemic core volume calculated by the Bayesian method and by the commonly used block-circulant singular value deconvolution technique. Read More

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October 2018

The role of acquisition and quantification methods in myocardial blood flow estimability for myocardial perfusion imaging CT.

Phys Med Biol 2018 09 13;63(18):185011. Epub 2018 Sep 13.

Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States of America.

In this work, we clarified the role of acquisition parameters and quantification methods in myocardial blood flow (MBF) estimability for myocardial perfusion imaging using CT (MPI-CT). We used a physiologic model with a CT simulator to generate time-attenuation curves across a range of imaging conditions, i.e. Read More

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September 2018

Enhancement of megavoltage electronic portal images for markerless tumor tracking.

J Appl Clin Med Phys 2018 Sep 9;19(5):398-406. Epub 2018 Jul 9.

Department of Radiation Oncology, Hallym University College of Medicine, Seoul, Korea.

Purpose: The poor quality of megavoltage (MV) images from electronic portal imaging device (EPID) hinders visual verification of tumor targeting accuracy particularly during markerless tumor tracking. The aim of this study was to investigate the effect of a few representative image processing treatments on visual verification and detection capability of tumors under auto tracking.

Methods: Images of QC-3 quality phantom, a single patient's setup image, and cine images of two-lung cancer patients were acquired. Read More

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September 2018

Hemodynamic response function (HRF) variability confounds resting-state fMRI functional connectivity.

Magn Reson Med 2018 10 15;80(4):1697-1713. Epub 2018 Apr 15.

Auburn University MRI Research Center, Department of Electrical and Computer Engineering, Auburn University, Auburn, Alabama.

Purpose: fMRI is the convolution of the hemodynamic response function (HRF) and unmeasured neural activity. HRF variability (HRFv) across the brain could, in principle, alter functional connectivity (FC) estimates from resting-state fMRI (rs-fMRI). Given that HRFv is driven by both neural and non-neural factors, it is problematic when it confounds FC. Read More

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October 2018