Usuario:Alexsavio

Alexandre Manhães Savio

• Contact: alexandre.manhaes__at__ehu.es

Studies

• Engineer in Computer Science (October 2006) - University of the Basque Country

• Currently: PhD Student in the Computational Intelligence Group of the Computer Science and Artificial Intelligence department - University of the Basque Country

Work Experience

• April/2007 - January/2008 - Software Engineer in InnovaeVision, San Sebastián, Guipúzcoa, Spain.

Java, Spring Framework, Hibernate, C/C++, GTK+, Cairo graphics, DirectFB

• July/2004 - April/2007 - Software Engineer in JADE Systems S.L., Zizur Mayor, Navarra, Spain.

C/C++, C++ Borland Builder 6, GUI design, Programming language parser (ANTLR), GNU/Linux Systems administration

Courses

• 7th-11th July, 2008 - AERFAI Summer School - PRMA'08 - Pattern Recognition for Motion Analysis in the Computer Vision Center of the Universidad Autónoma de Barcelona.

• 1st-12th July, 2009 - Athinoula A. Martinos Center for Biomedical Imaging, Boston, MA - Two-Week Multi-Modality Short Course

Publications

BibTex File

2009

Maite García-Sebastián, Alexandre Savio, Manuel Graña, Jorge Villanúa

On the use of Morphometry based features for Alzheimer's Disease detection on MRI

Bio-Inspired Systems: Computational and Ambient Intelligence. / IWANN 2009 (Part I)

Joan Cabestany, Francisco Sandoval, Alberto Prieto, Juan M. Corchado (Editors), LNCS 5517, Springer Verlag 2009, pp. 957-964

ISBN 978-3-642-02477-1

DOI 10.1007/978-3-642-02478-8_120

Data:

List of 98 OASIS females

Alexandre Savio, Maite García-Sebastián, Manuel Graña, Jorge Villanúa

Results of an Adaboost approach on Alzheimer's Disease detection on MRI

Methods and Models in Artificial and Natural Computation. / IWINAC 2009 (Part II)

José Mira, José Manuel Ferrández, José R. Álvarez, Félix de la Paz, F. Javier Toledo (Editors), LNCS 5602, Springer Verlag 2009, pp. 114-123

ISBN 978-3-642-02266-1

DOI 10.1007/978-3-642-02267-8_13

Data:

List of 98 OASIS females

Alexandre Savio, Maite García-Sebastián, Carmen Hernández, Manuel Graña, Jorge Villanúa

Classification Results of Artificial Neural Networks for Alzheimer's Disease Detection

Intelligent Data Engineering and Automated Learning - IDEAL 2009

LNCS 5788, Springer Verlag 2009, pp. 641-648

ISBN: 978-3-642-04393-2

DOI: 10.1007/978-3-642-04394-9_78

Data:

List of 98 OASIS females

2008

Maite García-Sebastián, A. M. Savio, M. Graña.

Comments on an Evolutionary Intensity Inhomogeneity Correction Algorithm [1]

Proceedings CEC 2008, pp.4146-4150

ISBN 978-1-4244-1822-0

Alexandre Manhaes Savio

Brain Image Registration - Capítulo de libro en las Actas de las II Jornadas de Inteligencia Computacional - JIC'08

Ramón Moreno Jiménez, Alexandre Manhaes Savio (Editors)

Servicio editorial de la UPV/EHU.

ISBN 978-84-296-2316-1

Projects

SAIOTEK 2008

• Desarrollo de métodos y técnicas de análisis de imagen de resonancia magnética cerebral en el ámbito del software libre para estudio de enfermedades neurodegenerativas (BRAINER) [2]
• Investigadora principal: Carmen Hernandez Gomez
• Entidades: Ciencias de la Computación e Inteligencia Artificial (UPV/EHU), Fundación Vasca de Innovación e Investigación Sanitaria/B+I+O (Eusko Fundazioa), Departamento de Neurociencia (UPV/EHU)
• Año Solicitud: 2.008 Fecha entrada: 19/02/09

Programa "Red guipuzcoana de Ciencia, Tecnología e Innovación" Gipuzkoako Foru Aldundia/Diputación Foral de Guipúzcoa

• Detección preclínica del Alzheimer mediante Neuroimagen [3]
• Referencia: OF145/2007
• Investigadora principal: Maite García-Sebastián
• Organismo: Universidad del País Vasco
• Duración: 1 año

SAIOTEK 2007

• Desarrollo de técnicas de análisis de imágenes de Resonancia Magnética con aplicación en el diagnóstico preclínico de la enfermedad de Alzheimer [4], [5]
• Referencia: S-PR07UN02
• Investigadora principal: Maite García-Sebastián
• Entidades participantes: UPV/EHU-Departamento de CCIA, Osatek-Gipuzkoa.
• Duración: 2 años

Otros proyectos del grupo [6]

Research Areas

• Pattern recognition applied to medical images
• Brain medical image processing
• Gesture recognition systems

Research Questions

• Mutual information non linear registration procedures.

• Steps of cortical surface registration. Cortical topology reconstruction.

• Tensor-based Morphometry

Pending Tasks

• ITK, ANTS...
• OpenMP and MPI
• Multivariate Analysis
• Meditate

Conferences

"I love deadlines. I especially like the whooshing sound they make as they go flying by." - Douglas Adams

Coming...

• ICPR 2010

Submission of full papers: Jan 15, 2010

• Workshop on Biomedical Image Registration

Paper submission deadline: 18 January 2010

Workshop date: 11 - 13 July 2010

Lübeck, Germany

• 2010 IEEE World Congress on Computational Intelligence

Paper Submission: January 31, 2010

Barcelona

• The 16th Annual Meeting of the Organization for Human Brain Mapping

Submission Opens: December 15

Abstract Deadline: January 29

Conference date: June 6-10, 2010

Barcelona

• MICCAI 2010

Submission of full papers: March 11, 2010

Conference date: September 20-24, 2010

Beijing, China

Current readings

Books

• Human Brain Function 2nd edition - J Ashburner, K Friston and W Penny PDF completo

• Medical Image Registration - by Joseph V. Hajnal (Editor), Derek L.G. Hill (Editor), David J. Hawkes (Editor)

• Splines - A perfect Fit for Signal and Image Processing

• Insight Into Images

• Numerical Methods for Image Registration - [7]

  @book{mcconnell_applications_1960,
        title = {Applications of Tensor Analysis},
        isbn = {0486603733},
        publisher = {Dover Publications},
        author = {A. J. {McConnell}},
        month = jun,
        year = {1960}
       }

Working articles

• COMPARE: Classification of Morphological Patterns Using Adaptive Regional Elements - Yong Fan, Dinggang Shen, Ruben C. Gur, Raquel E. Gur, Christos Davatzikos - IEEE Trans. Med. Imaging 26(1): 93-105 (2007)

• Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration - Arno Klein, Jesper Andersson, Babak A. Ardekani, John Ashburner, Brian Avants, Ming-Chang Chiang, Gary E. Christensen, Louis D. Collins, James Gee, Pierre Hellier, Joo Hyun Song, Mark Jenkinson, Claude Lepage, Daniel Rueckert, Paul Thompson, Tom Vercauteren, Roger P. Woods, J. John Mann, Ramin V. Parsey. NeuroImage (2009) DOI

• Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain - B.B. Avants, C.L. Epstein, M. Grossman and J.C. Gee. - Medical Image Analysis Volume 12, Issue 1, February 2008, Pages 26-41 - Special Issue on The Third International Workshop on Biomedical Image Registration – WBIR 2006

• A variational approach to multi-modal image matching - Hermosillo Gerardo; Chef d'Hotel Christophe; Faugeras Olivier - Variational and Level Set Methods in Computer Vision, 2001. Proceedings. IEEE Workshop on

• Point similarity measures for non-rigid registration of multi-modal data - Peter Rogelj, Stanislav Kovacic, James C. Gee, Computer Vision and Image UnderstandingVolume 92, Issue 1, , October 2003, Pages 112-140.

• Comparing Registration Methods for Mapping Brain Change using Tensor-Based Morphometry

• Mapping the regional influence of genetics on brain structure variability — A Tensor-Based Morphometry study

• More reading information in my groupware article Artículos Image Registration

Congresos y revistas objetivo

Revistas (ordenadas por factor de impacto)

1- Journal of Magnetic Resonance Imaging

2- Medical Image Analysis

3- IEEE Transactions of Medical Imaging

4- Magnetic Resonance in Medicine

Otras revistas

• Computer Assisted Radiology and Surgery

• Insight Journal

• Midas Journal

• Biomedical Imaging and Intervention Journal

• NeuroImage

• Brain

• Neural Computing and Applications

• Expert Systems and Applications

• Electronics Letters

• Artificial Intelligence in Medicine

• Cybernetics and Systems

Congresos

• MICCAI Society

• BIOSTEC

• SPIE Medical Imaging

• Computer Assisted Radiology and Surgery

• Human Brain Mapping

• Medical Informatics Europe Conference

• WBIR WBIR 2010

• More conferences: [8]

Internet Bookmarks

• CBU Imaging Wiki

• Kitware Youtube Channel

• BioInfoBank Library

• MindBoggle - A Project for Human Brain Labeling

• Supplementary Material Document from Klein NeuroImage 2009

• eigenfactor.org - ranking and mapping scientific knowledge

• Debian Neuroscience Repository

Courses

• Functional Magnetic Resonance Imaging: Data Acquisition and Analysis - MIT OpenCourseWare

• Cursos de formación

• Master en Iniciación a la Investigación en Matemáticas

Databases

• OASIS

• BrainMap

• Fractional Anisotropy Database

Research Groups

• Centre of Medical Image Computing - University College London - Gower Street - Eng. Building

• Structural Brain Mapping Group - University of Jena - Thüringen - central Germany

• Section of Biomedical Image Analysis - University of Pennsylvania

• Max Planck Institute für Hirnforschung

• Laboratorio de Imagen Médica. Unidad de Medicina y Cirugía Experimental - Hospital General Universitario Gregorio Marañón

• McConnell Brain Imaging Centre (BIC) of the Montreal Neurological Institute (MNI) - McGill University

• National Alliance for Medical Image Computing

• Asclepios project - INRIA Sophia-Antipolis

• ODYSSEE research project-team - INRIA Sophia-Antipolis

• Divisions of Bioimaging and MRI Technology - University and ETH Zurich

• Biomedical Imaging Group Rotterdam - Erasmus MC - University Medical Center Rotterdam

• A community portal for MIT brain research - Massachussets Institute of Technology

• Instituto Universitario de Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería - ULPGC

• Image Processing Lab de la FEI Sao Bernardo do Campo (SP) - Brasil

Utilities

Computer Settings

• Install Cisco VPN client on Ubuntu 8.04

• SPIE LaTEX manuscript templates and writing guidelines

• BibTeX Style Examples

• Impressive - The stylish way of giving PDF presentations

• Install ITK and Kitware software from sources. [9] [10] (for more information ask me)

• Install python wrapper on building ITK from sources.

• Create a 3DSlicer Plugin

• Sync Tomboy Notes

• Push references from JabRef to Lyx

• Página de instalación de FSL en Debian

• Setting up FSL to use a SunGridEngine or computing cluster

• How to install Springer LNCS Style for Lyx

• Automatically Generate a List of Publications for your CV

Image Processing

• Nomenclatura de los planos de corte en los seres vivos

• NA-MIC Software Repository

• ImageMagick Usage Examples

• FSL VBM How to

• BRAINSFit - Rigid Registration Tool

• Statistical Parametric Mapping

• SPM Programming Intro

• SPM5-Specific code snippets by John Ashburner

• A Quaternion and Rotation Primer

• FMRIB's Diffusion Toolbox - FDT v2.0

• 3D Slicer User Documentation

• Short introduction to DTI analysis

• Automatic Registration Toolbox (ART)

• A Quaternion and Rotation Primer

• Advanced Open Source Tools for Normalization and Neuroanatomy (SyN nonlinear registration algorithm)

• Semi-Automatic and Manual Segmentation of 3D Volumes

• Parallel Python for parallel processing

• Mask creation software for VBM analyses for SPM8

• Preprocessing steps for SPM Analyze images to use them on FSL

• fMRI methods

Pattern Recognition

• My scripts

• Weka How Tos

• Matrices de confusión y otros valores estadísticos

• LIBSVM - A library for Support Vector Machines

• Teach Me Data Analysis (Range scaling)

• Neural Networks - A Systematic Introduction

• Some interesting presentations

• Invited speakers for SIAM Conference on Optimization (Modersitzki presentation on image registration)

Real World

• Some useful hints to know about the PhD

• What the Simpsons think about graduate students!!

• Presentación de Luis Ibañez sobre el sin sentido del entorno de "ciencia abierta" en la que trabajamos. ( Página personal de Luis Ibañez en Kitware )

• Collaborative Research Initiatives

• Principios de colaboración abierta en la investigación (2005)

• Preguntas y respuestas sobre la situación Ingeniería Informática - Tratado de Bolonia, con referencias.

• 10 Reasons

• Visita al Instituto Nacional de Pesquisas Espaciais (INPE), Sao José Dos Campos (Brasil), Enero 2009

• Miguel's Photo gallery

Estado burocrático de la tesis

Director

Manuel Graña

Trabajo de investigación aprobado.

Contratos durante los años 2008 y 2009

Beca de Formación de Personal Investigador del Gobierno Vasco para los 4 años a partir del 2010.