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Accurate Segmentation of Brain MR Images
Accurate segmentation of brain MR images Master of Science Thesis in Biomedical Engineering ANTONIO REYES PORRAS PÉREZ Department of Signals and Systems Division of Biomedical Engineering CHALMERS UNIVERSITY OF TECHNOLOGY Göteborg, Sweden, 2010 Report No. EX028/2010 Abstract Full brain segmentation has been of significant interest throughout the years. Recently, many research groups worldwide have been looking into development of patient-specific electromagnetic models for dipole source location in EEG. To obtain this model, accurate segmentation of various tissues and sub-cortical structures is thus required. In this project, the performance of three of the most widely used software packages for brain segmentation has been analyzed: FSL, SPM and FreeSurfer. For the analysis, real images from a patient and a set of phantom images have been used in order to evaluate the performance r of each one of these tools. Keywords: dipole source location, brain, patient-specific model, image segmentation, FSL, SPM, FreeSurfer. Acknowledgements To my advisor, Antony, for his guidance through the project. To my partner, Koushyar, for all the days we have spent in the hospital helping each other. To the staff in Sahlgrenska hospital for their collaboration. To MedTech West for this opportunity to learn. Table of contents 1. Introduction ......................................................................................................................................... 1 2. Magnetic resonance imaging .............................................................................................................. -
1 Structural and Functional Alterations in the Brain Gray Matter
Structural and functional alterations in the brain gray matter among first-degree relatives of schizophrenia patients: a multimodal meta-analysis of fMRI and VBM studies Running title: Familial risk for schizophrenia and alterations in the brain Aino I. L. Saarinen, PhD1,2,3,*, Sanna Huhtaniska, MD, PhD4, Juho Pudas, MB3, Lassi Björnholm, MD3, Tuomas Jukuri, MD, PhD3, Jussi Tohka, MD, PhD5, Niklas Granö, PhD6, Jennifer H. Barnett, PhD7,8, Vesa Kiviniemi, MD, PhD9,10, Juha Veijola, MD, PhD3,10,11, Mirka Hintsanen, PhD1, Johannes Lieslehto, MD, PhD 12 1 Research Unit of Psychology, University of Oulu, Finland 2 Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland 3 Research Unit of Clinical Neuroscience, Department of Psychiatry, University of Oulu, Finland 4 Center for Life Course Health Research, University of Oulu, Finland 5 A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland 6 Helsinki University Hospital, Department of Adolescent Psychiatry, Finland 7 Cambridge Cognition, Cambridge, UK 8 Department of Psychiatry, University of Cambridge, Cambridge, UK 9 Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland 10 Department of Psychiatry, Oulu University Hospital, Oulu, Finland 11 Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland 12 Section for Neurodiagnostic Applications, Department of Psychiatry, Ludwig Maximilian University, Nussbaumstrasse 7, 80336 Munich, Bavaria, * Corresponding author: Aino Saarinen. Department of Psychology and Logopedics, Faculty of Medicine, Haartmaninkatu 3, P.O. Box 21, 00014 University of Helsinki, Finland. E-mail: [email protected], Tel.: +35844 307 1204. 1 Abstract Objective: Schizophrenia has one of the highest heritability estimates in psychiatry, but the genetically- based underlying neuropathology has mainly remained unclear. -
Simultaneous PET/MRI for Connectivity Mapping: Quantitative Methods in Clinical Setting
UNIVERSITY OF PADOVA Department of Information Engineering Ph.D. School on Information Engineering Curriculum: Bioengineering - Cycle: XXX Simultaneous PET/MRI for Connectivity Mapping: Quantitative Methods in Clinical Setting Headmaster of the School: Prof. Andrea NEVIANI Supervisor: Prof. Alessandra BERTOLDO PhD. Candidate: Eng. Erica SILVESTRI 2018 iii University of Padova Abstract Ph.D. School on Information Engineering Simultaneous PET/MRI for Connectivity Mapping: Quantitative Methods in Clinical Setting by Eng. Erica SILVESTRI In recent years, the study of brain connectivity has received growing inter- est from neuroscience field, from a point of view both of analysis of patho- logical condition and of a healthy brain. Hybrid PET/MRI scanners are promising tools to study this complex phenomenon. This thesis presents a general framework for the acquisition and analysis of simultaneous multi- modal PET/MRI imaging data to study brain connectivity in a clinical set- ting. Several aspects are faced ranging from the planning of an acquisition protocol consistent with clinical constraint to the off-line PET image recon- struction, from the selection and implementation of methods for quantifying the acquired data to the development of methodologies to combine the com- plementary informations obtained with the two modalities. The developed analysis framework was applied to two different studies, a first conducted on patients affected by Parkinson’s Disease and dementia, and a second one on high grade gliomas, as proof of concept evaluation that the pipeline can be extended in clinical settings. v Università degli Studi di Padova Sommario Scuola di Dottorato in Ingegneria dell’Informazione Acquisizioni simultanee PET/MR per lo studio della connettività: metodi quantitativi in ambito clinico di Ing. -
Omar Bagasra (1948-Present)
Omar Bagasra (1948-Present) Professor of Biology Claflin University Director South Carolina Center for Biotechnology “I know I’m making a difference in other people’s lives.” Omar Bagasra, 2006. Overview Dr. Omar Bagasra is a professor of biology at Claflin University, a historically black university in Orangeburg, South Carolina, and is also the founder and director of the South Carolina Center for Biotechnology. His research combines environmental medicine with molecular biology and health disparity issues. Bagasra is particularly interested in finding out why African Americans have the highest rates of prostate cancer (as well as diabetes, hypertension, and female breast cancer) in the world. He has also made a notable contribution to his field by discovering in situ PCR, which allows researchers to determine the percentage of HIV-infected cells in a body. His other areas of interest include: • A Unified Concept of HIV Latency • An Edible Vacine for Malaria Using Transgenic Tomatoes • Role of Micro-RNAs in Regulation of Lentiviral Latency and Persistence. • Locatization of human herpesvirus type 8 in human sperms by in situ PCR. • RNAi as Antiviral Therapy • Zinc and prostate cancer • Role of zinc and zinc transporters in the molecular pathogenesis of diabetes mellitus. Bagasra says that this life-long intellectual curiosity keeps him in the environmental field. Early Life and Career Omar Bagasra was born on October 9, 1948, on the plains of India. He is the eldest of Amina and Habib Bagasra’s eleven children. Just prior to his birth, India gained independence from Great Britain, and Bagasra’s family joined an exodus of twenty-five million people who left India for the newly-formed nation of Pakistan. -
CURRICULUM VITAE Omar Bagasra, MD, Ph.D. Professor of Biology
Omar Bagasra, M.D., Ph.D. CURRICULUM VITAE Omar Bagasra, M.D., Ph.D. Professor of Biology Director South Carolina Center for Biotechnology Claflin University Orangeburg, SC 29115 E-mail:[email protected] [email protected] Links: www.omarbagasra.com https://en.wikipedia.org/wiki/Omar_Bagasra 1 Omar Bagasra, M.D., Ph.D. CURRICULUM VITAE Personal Information Name: Omar Bagasra, M.D., Ph.D. Current Titles: Professor of Biology (with Tenure) Director, South Carolina Center for Biotechnology 400 Magnolia Street, Claflin University, Orangeburg, SC 29115, USA Clinical Professor of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine Columbia, SC 29208. 2002-2016 Adjunct Professor. Department of Epidemiology & Biostatistics School of Public Health, Univ. of South Carolina Columbia, SC 29208, USA 2002-2016 Adjunct Professor Department of Pathology Dow University of Health Science Karachi, Pakistan 2011-present Visiting Professor Microbiology & Immunology Universidad Autonoma de Guadalajara, Mexico 2006-2012 Office: TEL: 803-535-5253 FAX: 803-535-5776 Cell: 803-707-8933 (for private calls) E-mail: [email protected] [email protected] Home Address: 205 Hawk Chase Drive Orangeburg, SC 29115 Tel: 803-516-9758 Citizenship: The United States of America (since 1981) 2 Omar Bagasra, M.D., Ph.D. Place of Birth: Bagasra (Junagadh State), India Education 1968 B.Sc in Microbiology University of Karachi, Pakistan 1970 M.Sc. in Biochemistry University of Karachi, Pakistan 1979 Ph.D. in Microbiology & Immunology -
A Simple Rapid Process for Semi-Automated Brain Extraction from Magnetic Resonance Images of the Whole Mouse Head
Accepted Manuscript Title: A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head Author: Adam Delora Aaron Gonzales Christopher S. Medina Adam Mitchell Abdul Faheem Mohed Russell E. Jacobs Elaine L. Bearer PII: S0165-0270(15)00370-2 DOI: http://dx.doi.org/doi:10.1016/j.jneumeth.2015.09.031 Reference: NSM 7360 To appear in: Journal of Neuroscience Methods Received date: 10-8-2015 Revised date: 28-9-2015 Accepted date: 30-9-2015 Please cite this article as: Delora A, Gonzales A, Medina CS, Mitchell A, Mohed AF, Jacobs RE, Bearer EL, A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head, Journal of Neuroscience Methods (2015), http://dx.doi.org/10.1016/j.jneumeth.2015.09.031 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Graphical Abstract (for review) Accepted Manuscript Page 1 of 27 A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head Delora, Gonzales, Medina, Mitchell, Mohed, Jacobs and Bearer Highlights • We present a new software tool for automated mouse brain extraction • The new software tool is rapid and applies to any MR dataset • We validate the output by comparing with manual extraction (the gold standard) • Brain extraction with this tool preserves individual volume, and improves alignments Accepted Manuscript Page 2 of 27 Fast automated skull-stripping Delora et al. -
2013 Faseb Science Research Conferences Advisory Committee Meeting
Proposal #: 15-05 2013 FASEB SCIENCE RESEARCH CONFERENCES ADVISORY COMMITTEE MEETING TOPIC FOR CONSIDERATION TOPIC NAME: GASTROINTESTINAL TRACT XVI. GI HOMEOSTASIS: THE MICROBIOME AND THE BARRIER, DEVELOPMENT AND DISEASE PREVIOUS TITLE: Gastrointestinal Tract XV: Epithelia, Microbes, Inflammation and Cancer SUBMITTED BY: Richard M. Peek, Jr., Vanderbilt University Medical Center Jason Mills, Washington University School of Medicine Melissa H. Wong, Oregon Health & Science University YEAR REQUESTED FOR SCHEDULING: 2015 SITE REQUESTS: 1. Steamboat Springs, CO 2. Big Sky, MT 3. Keystone, CO DATE REQUESTS: 1. August 9-14, 2015 2. August 16-21, 2015 3. August 2-7, 2015 YEAR(S) CONFERENCE HAS BEEN HELD: 1985, 1987, 1989, 1991, 1993, 1995, 1997, 1999, 2001, 2003, 2005, 2007, 2009, 2011, 2013 NOTES: To the best of our knowledge, there is not a direct conflict with any other FASEB SRC or other society or industry meeting. 2015 FASEB Summer Research Conference Proposal Gastrointestinal Tract XVI. GI homeostasis: The microbiome and the barrier, development and disease Section 2: Conference Title & Organizer Information: TITLE OF CONFERENCE: Gastrointestinal Tract XVI. GI homeostasis: The microbiome and the barrier, development and disease # of EXPECTED ATTENDEES: 160 Preferred Primary Point of Contact for Proposal Questions: Dr. Richard M. Peek, Jr. Professor of Medicine and Cancer Biology Director, Division of Gastroenterology, Hepatology and Nutrition Vanderbilt University Medical Center 2215 Garland Avenue, 1030C MRB IV Nashville, TN 37232, USA -
Software Tools for the Analysis of Functional Magnetic Resonance Imaging
Basic and Clinical Autumn 2012, Volume 3, Number 5 Software Tools for the Analysis of Functional Magnetic Resonance Imaging Mehdi Behroozi 1,2, Mohammad Reza Daliri 1* 1. Biomedical Engineering Department, Faculty of Electrical Engineering, Iran University of Science and Technology (IUST), Tehran, Iran. 2. School of Cognitive Sciences (SCS), Institute for Research in Fundamental Science (IPM), Niavaran, Tehran, Iran. Article info: A B S T R A C T Received: 12 July 2012 First Revision: 7 August 2012 Functional magnetic resonance imaging (fMRI) has become the most popular method for Accepted: 25 August 2012 imaging of brain functions. Currently, there is a large variety of software packages for the analysis of fMRI data, each providing many features for users. Since there is no single package that can provide all the necessary analyses for the fMRI data, it is helpful to know the features of each software package. In this paper, several software tools have been introduced and they Key Words: have been evaluated for comparison of their functionality and their features. The description of fMRI Software Packages, each program has been discussed and summarized. Preprocessing, Segmentation, Visualization, Registration. 1. Introduction analysis the fMRI data to extract information about the different stimuli (Matthews, Shehzad, & Kelly, 2006). unctional Magnetic resonance imaging (fMRI), a modern technique of imaging, is a Generated data from fMRI have very large amount. powerful non-invasive and safe tool which The handling, processing, analysis and visualization Downloaded from bcn.iums.ac.ir at 18:01 CET on Friday February 20th 2015 F is used for the study of the function of the of fMRI data are not feasible without computer-based brain based on measure of the brain neural methods. -
Chicago 2013 Final Program
CHICAGO 2013 FINAL PROGRAM 2013 Combined Annual Meeting of Central Society for Clinical and Translational Research and Midwestern Section American Federation for Medical Research Renaissance Blackstone Chicago CHICAGO, IL • APRIL 25-26, 2013 Jointly prese nted by CS CTR, M WAF MR a nd I nstit ute for t he A dvan ceme nt of Huma n Behav ior (IAHB) Central Society for Clinical and Translational Research 555 East Wells Street Suite 1100 Milwaukee, WI 53202 Phone 414.273.2209 Fax 414.276.3349 Web www.CSCR.com Midwestern Section American Federation for Medical Research 500 Cummings Center - Suite 4550 Beverly, MA 01915 Phone 978.927.8330 Fax 978.524.8890 Web www.afmr.org 2013 Combined Annual Meeting Learning Objectives This activity has been planned and implemented in accordance The 2013 Combined Annual Meeting of the Central Society with the Essential Areas and Policies of the Accreditation for Clinical and Translational Research (CSCTR) and the Council for Continuing Medical Education through the Midwestern Section American Federation for Medical Research joint sponsorship of the Institute for the Advancement of (MWAFMR) presents the Hickam Lecture, Keynote Speaker, Human Behavior (IAHB) and Central Society for Clinical and two plenary sessions and an oral abstract session on topics Translational Research and American Federation for Medical of timely interest for researchers and physicians interested in Research. [IAHB] is accredited by the ACCME to provide the broad field of clinical research. Participants at the 2013 continuing medical education for physicians. Combined Annual Meeting will acquire knowledge into clinical Credit Designation Statement research techniques and new findings in various aspects of internal medicine and other fields. -
A Study on the Core Area Image Processing: Current Research
The International journal of analytical and experimental modal analysis ISSN NO: 0886-9367 A Study on the Core Area Image Processing: Current Research, Softwares and Applications K.Kanimozhi1, Dr.K.Thangadurai2 1Research Scholar, PG and Research Department of Computer Science, Government Arts College, Karur-639005 2Assistant professor and Head, PG and Research Department of Computer Science, Government Arts College, Karur-639005 [email protected] [email protected] Abstract —Among various core subjects such as, networking, data mining, data warehousing, cloud computing, artificial intelligence, image processing, place a vital role on new emerging ideas. Image processing is a technique to perform some operations with an image to get its in enhanced version or to retrieve some information from it. The image can be of signal dispension, video for frame or a photograph while the system treats that as a 2D- signal. This image processing area has its applications in various wide range such as business, engineering, transport systems, remote sensing, tracking applications, surveillance systems, bio medical fields, visual inspection systems etc.., Its purpose can be of: to create best version of images(image sharpening and restoring), retrieving of images, pattern measuring and recognizing images. Keywords — Types, Flow, Projects, MATLAB, Python. I. INTRODUCTION In computer concepts, digital image processing technically means that of using computer algorithms to process digital images. Initially in1960’s the image processing had been applied for those highly technical applications such as satellite imagery, medical imaging, character recognition, wire-photo conversion standards, video phone and photograph enhancement. Since the cost of processing those images was very high however with the equipment used too. -
LONI Pipeline Handbook
LONI Pipeline Neuroimaging Solutions A practical, hands-on guide to using the LONI Pipeline for neuroimaging analysis LONI Pipeline version 7.0.1 Handbook version 1.6 http://pipeline.loni.usc.edu LONI Pipeline training is funded by the National Institutes of Health through NIBIB grant P41EB015922 Contents Getting Started 1 Overview: About LONI Pipeline 1 Benefits 1 Requirements 1 Installation 2 Software Download 2 LONI Cluster Usage Account 2 Platform-Specific Installation 2 OS X 2 Windows 3 Linux/Unix 3 Interface 4 Overview 4 Data Sources & Sinks 6 Overview 6 How-to 6 Find & Replace 7 LONI Pipeline Viewer 8 Overview 8 Beginning Example Workflows 9 Registration Using AIR 10 Image Processing with the Quantitative Imaging Toolkit - Denoising 29 Intermediate Topics 37 LONI Image Data Archive 38 Overview 38 Change Server for Entire Workflow 40 Overview 40 How-to 40 Intermediate Example Workflows 41 fMRI First Level Analyses 42 DTI Analyses 59 DSI Analyses 65 Image Analysis with the Quantitative Imaging Toolkit - Tractography Metrics 73 Advanced Topics 85 Building a Module 86 Overview 86 How-to 86 Optional Actions 87 Required Options 88 Adding additional parameters 90 Specify dependencies and manipulate file names 90 LONI Pipeline Provenance 92 Overview 92 How-to 92 Adding Metadata 95 Overview 95 How-to 96 Conditional Module 98 Overview 98 How-to 98 Distributed Pipeline Server Installation 102 Introduction 102 GUI Installation 102 Command Line Installation 110 Glossary 113 Bibliography 116 Getting Started Overview: About LONI Pipeline The LONI Pipeline is a free workflow application primarily aimed at neuroimaging researchers. With the LONI Pipeline, users can quickly create workflows that take advantage of any and all neuroimaging tools available. -
What Is Function?
What is Function? From organelles to organisms, Function seeks papers that contribute to defining the mechanistic basis of living systems in health and disease. Function aims to be a highly selective journal, publishing major advances that extend physiological understanding of biological function and the changes associated with disease states. Why Function? Why Now? The American Physiological Society (APS) developed Function to provide a new home for authors—members and nonmembers—who welcome a fresh, multidisciplinary option for publishing their most important physiology research. What Makes Function Unique? Function will be unique as an open access, high-profile physiology journal that is society-owned and edited by working scientists. New features have been added to expediate the publication of the most important physiology research. New Features FUNCTION FOCUS PERSPECTIVE ARTICLES This new type of short focus article reports For full original research articles, Function on a new and important observation. These will include a perspective, opinion, or “quick release” articles allow for solid research commentary article from a top expert in the to be reported without all the ramifications field providing an elevated point of view on expected in a full research paper. the scientific impact of the article. NEW STYLE EVIDENCE REVIEWS FINAL DECISION AFTER INITIAL REVIEW These articles will evaluate the factual Submitting authors will receive a firm new style evidence in a field and therefore only cite decision about acceptance or rejection after original articles and not other reviews. the initial review, even if revisions are needed. Learn more and submit at journals.physiology.org/function. Questions? Contact [email protected].