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    Minimization of target registration error for vertebra in image-guided spine surgery

    , Article International Journal of Computer Assisted Radiology and Surgery ; Vol. 9, issue. 1 , January , 2014 , p. 29-38 Ershad, M ; Ahmadian, A ; Dadashi Serej, N ; Saberi, H ; Amini Khoiy, K ; Sharif University of Technology
    Abstract
    Purpose: The accuracy of pedicle screw placement during image-guided spine surgery (IGSS) can be characterized by estimating the target registration error (TRE). The major factors that influence TRE were identified, minimized, and verified with in vitro experiments. Materials and methods: Computed-tomography- compatible markers are placed over anatomical landmarks of lumbar vertebral segments in locations that are feasible and routinely used in surgical procedures. TRE was determined directly for markers placed on the pedicles of vertebra segments. First, optimum selections of landmarks are proposed for different landmarks according to the minimum achievable TRE values in different... 

    An implementation of a CBIR system based on SVM learning scheme

    , Article Journal of Medical Engineering and Technology ; Volume 37, Issue 1 , 2013 , Pages 43-47 ; 03091902 (ISSN) Tarjoman, M ; Fatemizadeh, E ; Badie, K ; Sharif University of Technology
    2013
    Abstract
    Content-based image retrieval (CBIR) has been one of the most active areas of research. The retrieval principle of CBIR systems is based on visual features such as colour, texture and shape or the semantic meaning of the images. A CBIR system can be used to locate medical images in large databases. This paper presents a CBIR system for retrieving digital human brain magnetic resonance images (MRI) based on textural features and the support vector machine (SVM) learning method. This system can retrieve similar images from the database in two groups: normal and tumoural. This research uses the knowledge of the CBIR approach to the application of medical decision support and discrimination... 

    Design of linear anti-scatter grid geometry with optimum performance for screen-film and digital mammography systems

    , Article Physics in Medicine and Biology ; Volume 60, Issue 15 , July , 2015 , Pages 5753-5765 ; 00319155 (ISSN) Khodajou Chokami, H ; Sohrabpour, M ; Sharif University of Technology
    Institute of Physics Publishing  2015
    Abstract
    A detailed 3D Monte Carlo simulation of the grid geometrical parameters in screen-film mammography (SFM) and digital mammography (DM) systems has been performed. A combination of IEC 60627:2013 international standard conditions and other more clinically relevant parameters were used for this simulation. Accuracy of our results has been benchmarked with previously published data and good agreement has been obtained. Calculations in a wide range of linear anti-scatter grid geometries have been carried out. The evaluated parameters for the SFM system were the Bucky factor (BF) and contrast improvement factor (CIF) and for the DM system it was signal differenceto- noise ratio improvement factor... 

    Intensity estimation of spontaneous facial action units based on their sparsity properties

    , Article IEEE Transactions on Cybernetics ; Volume 46, Issue 3 , 2016 , Pages 817-826 ; 21682267 (ISSN) Mohammadi, M. R ; Fatemizadeh, E ; Mahoor, M. H ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2016
    Abstract
    Automatic measurement of spontaneous facial action units (AUs) defined by the facial action coding system (FACS) is a challenging problem. The recent FACS user manual defines 33 AUs to describe different facial activities and expressions. In spontaneous facial expressions, a subset of AUs are often occurred or activated at a time. Given this fact that AUs occurred sparsely over time, we propose a novel method to detect the absence and presence of AUs and estimate their intensity levels via sparse representation (SR). We use the robust principal component analysis to decompose expression from facial identity and then estimate the intensity of multiple AUs jointly using a regression model... 

    Directed functional networks in Alzheimer's disease: disruption of global and local connectivity measures

    , Article IEEE Journal of Biomedical and Health Informatics ; Volume 21, Issue 4 , 2017 , Pages 949-955 ; 21682194 (ISSN) Afshari, S ; Jalili, M ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2017
    Abstract
    Techniques available in graph theory can be applied to signals recorded from human brain. In network analysis of EEG signals, the individual nodes are EEG sensor locations and the edges correspond to functional relations between them that are extracted from EEG time series. In this paper, we study EEG-based directed functional networks in Alzheimer's disease (AD). To this end, directed connectivity matrices of 25 AD patients and 26 healthy subjects are processed and a number of meaningful graph theory metrics are studied. Our data show that functional networks of AD brains have significantly reduced global connectivity in alpha and beta bands (P < 0.05). The AD brains have significantly... 

    Cardiac contraction motion compensation in gated myocardial perfusion SPECT: a comparative study

    , Article Physica Medica ; Volume 49 , 2018 , Pages 77-82 ; 11201797 (ISSN) Salehi, N ; Rahmim, A ; Fatemizadeh, E ; Akbarzadeh, A ; Farahani, M. H ; Farzanefar, S ; Ay, M. R ; Sharif University of Technology
    Associazione Italiana di Fisica Medica  2018
    Abstract
    Introduction: Cardiac contraction significantly degrades quality and quantitative accuracy of gated myocardial perfusion SPECT (MPS) images. In this study, we aimed to explore different techniques in motion-compensated temporal processing of MPS images and their impact on image quality and quantitative accuracy. Material and method: 50 patients without known heart condition underwent gated MPS. 3D motion compensation methods using Motion Freezing by Cedars Sinai (MF), Log-domain Diffeomorphic Demons (LDD) and Free-Form Deformation (FFD) were applied to warp all image phases to fit the end-diastolic (ED) phase. Afterwards, myocardial wall thickness, myocardial to blood pool contrast, and... 

    Optical radiomic signatures derived from optical coherence tomography images improve identification of melanoma

    , Article Cancer Research ; Volume 79, Issue 8 , 2019 , Pages 2021-2030 ; 00085472 (ISSN) Turani, Z ; Fatemizadeh, E ; Blumetti, T ; Daveluy, S ; Moraes, A. F ; Chen, W ; Mehregan, D ; Andersen, P. E ; Nasiriavanaki, M ; Sharif University of Technology
    American Association for Cancer Research Inc  2019
    Abstract
    The current gold standard for clinical diagnosis of melanoma is excisional biopsy and histopathologic analysis. Approximately 15–30 benign lesions are biopsied to diagnose each melanoma. In addition, biopsies are invasive and result in pain, anxiety, scarring, and disfigurement of patients, which can add additional burden to the health care system. Among several imaging techniques developed to enhance melanoma diagnosis, optical coherence tomography (OCT), with its high-resolution and intermediate penetration depth, can potentially provide required diagnostic information noninvasively. Here, we present an image analysis algorithm, "optical properties extraction (OPE)," which improves the... 

    Subject-specific loads on the lumbar spine in detailed finite element models scaled geometrically and kinematic-driven by radiography images

    , Article International Journal for Numerical Methods in Biomedical Engineering ; Volume 35, Issue 4 , 2019 ; 20407939 (ISSN) Dehghan Hamani, I ; Arjmand, N ; Shirazi Adl, A ; Sharif University of Technology
    Wiley-Blackwell  2019
    Abstract
    Traditional load-control musculoskeletal and finite element (FE) models of the spine fail to accurately predict in vivo intervertebral joint loads due mainly to the simplifications and assumptions when estimating redundant trunk muscle forces. An alternative powerful protocol that bypasses the calculation of muscle forces is to drive the detailed FE models by image-based in vivo displacements. Development of subject-specific models, however, both involves the risk of extensive radiation exposures while imaging in supine and upright postures and is time consuming in terms of the reconstruction of the vertebrae, discs, ligaments, and facets geometries. This study therefore aimed to introduce a... 

    In silico study of patient-specific magnetic drug targeting for a coronary LAD atherosclerotic plaque

    , Article International Journal of Pharmaceutics ; Volume 559 , 2019 , Pages 113-129 ; 03785173 (ISSN) Shamloo, A ; Amani, A ; Forouzandehmehr, M ; Ghoytasi, I ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Coronary artery disease is the first cause of death across the world. Targeted delivery of therapeutics through controlled release of micro- and nano-particles remains a very capable approach to develop new strategies in treating restenosis and atherosclerotic plaques. In this research, to produce the arterial geometry, an image-processing was done using CT-scan images of a LAD coronary artery. After implementing the finite element mesh, the Fluid-Structure Interaction (FSI) simulation based on physiological boundary conditions was performed. Next, a Lagrangian description of particles dynamics in a non-Newtonian blood flow considering momentum equation of motion for each particle and the... 

    Bilayered heparinized vascular graft fabricated by combining electrospinning and freeze drying methods

    , Article Materials Science and Engineering C ; Volume 94 , 2019 , Pages 1067-1076 ; 09284931 (ISSN) Khayat Norouzi, S ; Shamloo, A ; Sharif University of Technology
    Elsevier Ltd  2019
    Abstract
    Small diameter vascular grafts (<6 mm) are highly demanded for patients suffering from severe occluded arteries to be used as a bypass or substituted conduit. Fabricating a graft with appropriate structural, mechanical and cell growth properties which has simultaneously anti-thrombogenic trait is a challenge nowadays. Here, we proposed a bilayer heparinized vascular graft that can mimic the structural and mechanical characteristics close to those of the native coronary artery by combining electrospinning and freeze drying methods. In this study, the inner layer was made by co-electrospinning of synthetic polymer, poly-caprolactone (PCL) and the natural polymer, gelatin (Gel). Also, heparin... 

    Bilayered heparinized vascular graft fabricated by combining electrospinning and freeze drying methods

    , Article Materials Science and Engineering C ; Volume 94 , 2019 , Pages 1067-1076 ; 09284931 (ISSN) Khayat Norouzi, S ; Shamloo, A ; Sharif University of Technology
    Elsevier Ltd  2019
    Abstract
    Small diameter vascular grafts (<6 mm) are highly demanded for patients suffering from severe occluded arteries to be used as a bypass or substituted conduit. Fabricating a graft with appropriate structural, mechanical and cell growth properties which has simultaneously anti-thrombogenic trait is a challenge nowadays. Here, we proposed a bilayer heparinized vascular graft that can mimic the structural and mechanical characteristics close to those of the native coronary artery by combining electrospinning and freeze drying methods. In this study, the inner layer was made by co-electrospinning of synthetic polymer, poly-caprolactone (PCL) and the natural polymer, gelatin (Gel). Also, heparin... 

    Extraction and automatic grouping of joint and individual sources in multisubject fMRI data using higher order cumulants

    , Article IEEE Journal of Biomedical and Health Informatics ; Volume 23, Issue 2 , 2019 , Pages 744-757 ; 21682194 (ISSN) Pakravan, M ; Shamsollahi, M. B ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Abstract
    The joint analysis of multiple data sets to extract their interdependency information has wide applications in biomedical and health informatics. In this paper, we propose an algorithm to extract joint and individual sources of multisubject data sets by using a deflation-based procedure, which is referred to as joint/individual thin independent component analysis (JI-ThICA). The proposed algorithm is based on two cost functions utilizing higher order cumulants to extract joint and individual sources. Joint sources are discriminated by fusing signals of all subjects, whereas individual sources are extracted separately for each subject. Furthermore, JI-ThICA algorithm estimates the number of... 

    Combining multivariate image analysis with high-performance thin-layer chromatography for development of a reliable tool for saffron authentication and adulteration detection

    , Article Journal of Chromatography A ; Volume 1628 , 2020 Amirvaresi, A ; Rashidi, M ; Kamyar, M ; Amirahmadi, M ; Daraei, B ; Parastar, H ; Sharif University of Technology
    Elsevier B.V  2020
    Abstract
    In this work, high-performance thin-layer chromatography (HPTLC) coupled with multivariate image analysis (MIA) is proposed as a fast and reliable tool for authentication and adulteration detection of Iranian saffron samples based on their HPTLC fingerprints. At first, the secondary metabolites of saffron were extracted using ultrasonic-assisted solvent extraction (UASE) which was optimized using central composite design (CCD). Next, the RGB coordinates of HPTLC images were used for estimation of saffron origin based on principal component analysis (PCA). The PCA scores plot showed that saffron samples were clustered into two clear-cut groups which was 92% matched with the geographical... 

    3D Image Segmentation with Sparse Annotation by Self-Training and Internal Registration

    , Article IEEE Journal of Biomedical and Health Informatics ; Volume 25, Issue 7 , 2021 , Pages 2665-2672 ; 21682194 (ISSN) Bitarafan, A ; Nikdan, M ; Baghshah, M. S ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2021
    Abstract
    Anatomical image segmentation is one of the foundations for medical planning. Recently, convolutional neural networks (CNN) have achieved much success in segmenting volumetric (3D) images when a large number of fully annotated 3D samples are available. However, rarely a volumetric medical image dataset containing a sufficient number of segmented 3D images is accessible since providing manual segmentation masks is monotonous and time-consuming. Thus, to alleviate the burden of manual annotation, we attempt to effectively train a 3D CNN using a sparse annotation where ground truth on just one 2D slice of the axial axis of each training 3D image is available. To tackle this problem, we propose... 

    Using distance on the Riemannian manifold to compare representations in brain and in models

    , Article NeuroImage ; Volume 239 , 2021 ; 10538119 (ISSN) Shahbazi, M ; Shirali, A ; Aghajan, H ; Nili, H ; Sharif University of Technology
    Academic Press Inc  2021
    Abstract
    Representational similarity analysis (RSA) summarizes activity patterns for a set of experimental conditions into a matrix composed of pairwise comparisons between activity patterns. Two examples of such matrices are the condition-by-condition inner product and correlation matrix. These representational matrices reside on the manifold of positive semidefinite matrices, called the Riemannian manifold. We hypothesize that representational similarities would be more accurately quantified by considering the underlying manifold of the representational matrices. Thus, we introduce the distance on the Riemannian manifold as a metric for comparing representations. Analyzing simulated and real fMRI...