Usuario:Alexsavio

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Material

Seguimientos

Pedradas

Surveys (wiki under construction)

Alexandre Manhães Savio

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++ in GNU/Linux, GTK 2, 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

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

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

• May 31st - June 4th, 2010 - FSL Course organised by FMRIB, Oxford, the Martinos Center, MGH and Heidelberg & Würzburg Universities in Heidelberg, Germany.

Internships

• January 24th - July 31st, 2011 - FMRIB, University of Oxford, UK with Dr. Saad Jbabdi. On ball&stick diffusion models for multishell HARDI and model selection.

Publications

BibTex File

2011

Deformation based features for Alzheimer's disease detection with linear SVM.

Alexandre Savio, Manuel Graña, Jorge Villanúa.

Hybrid Artificial Intelligence Systems, 6th International Conference (HAIS 2011) - HAIS 2011, Part II, LNAI 6679 proceedings, p.336-343. Springer, Heidelberg (2011)

• draft
• Deformation features

2010

Neurocognitive disorder detection based on Feature Vectors extracted from VBM analysis of structural MRI

Alexandre Savio; Maria T García-Sebastián; Darya Chyzhyk; Carmen Hernández; Manuel Graña; Andone Sistiaga; Adolfo Lopez de Munain; Jorge Villanúa

Computers in Biology and Medicine (accepted: CBM-D-10-00306R1)

Indice de Impacto JCR (2009) 1.269

Neural classifiers for schizophrenia diagnostic support on diffusion imaging data

Alexandre Savio, Juliette Charpentier, Maite Termenón, Ann K. Shinn, Manuel Graña

Neural Network World 20(7):935-949 [1].

ISI JCR 2009: 0.475

• slides

Data:

• Post-processed subjects: part 1, part 2 and part 3
• Correlation values: part 1, part 2 and part 3
• Feature masks
• Features vectors

• Data extracted from the NAMIC: Brain Multimodality database.

A Comparison of VBM Results by SPM, ICA and LICA

Darya Chyzyk, Maite Termenón, Alexandre Savio

Hybrid Artificial Intelligence Systems, 5th International Conference / HAIS 2010, San Sebastián, Spain, June 23-25, 2010. Proceedings, Part II

Emilio Corchado and Manuel Graña Romay and Alexandre Manhaes Savio, LNCS 6077, Springer Verlag 2010, pp. 429-435

ISBN: 978-3-642-13802-7

DOI 10.1007/978-3-642-13803-4_53

2009

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

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

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

• draft

Data:

List of 98 OASIS females

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

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

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

draft

Data:

List of 98 OASIS females

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

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

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

draft

Data:

List of 98 OASIS females

2008

Comments on an Evolutionary Intensity Inhomogeneity Correction Algorithm

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

| link

Proceedings CEC 2008, pp.4146-4150

ISBN 978-1-4244-1822-0

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

Alexandre Manhaes Savio

Ramón Moreno Jiménez, Alexandre Manhaes Savio (Editors)

Servicio editorial de la UPV/EHU.

ISBN 978-84-296-2316-1

slides_book

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

• How does the multivariate tensor analysis work using all the deformation tensor information?

• Is there any SOM-based framework for diffusion data modelling?

• Any application of Lattice-Computing on Probabilistic Tractography?

Pending Tasks

• ITK, ANTS...
• OpenMP and MPI
• Multivariate Analysis
• Meditate
• DTI modeling
• Process Ann's DTI dataset
• Add MRI and ML related info pages with literature reviews on this wiki.

Conferences

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

Coming...

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

• More information in my groupware articles Artículos Image Registration and Working Diaries

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

• Neuroimage

• Computer Assisted Radiology and Surgery

• Insight Journal

• Midas Journal

• Biomedical Imaging and Intervention Journal

• Brain

• Neural Computing and Applications

• Expert Systems and Applications

• Electronics Letters

• Artificial Intelligence in Medicine

• Cybernetics and Systems

• Neuroscience Letters

Congresos

• MICCAI Society

• BIOSTEC

• ISMRM

• 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

• INDI - 1000 Functional Connectomes Project

• ADNI

• BrainMap

• Fractional Anisotropy Database

• MIDAS

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

Scientific Writing

• Chapter "How to Write an Introduction" of Professor Glasman-Deal's Science Research Writing For Non-Native Speakers of English ( Ref. )

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

• Setting up a Ubuntu 10.04.1 cluster (NFS, NIS, Sun Grid Engine, FSL) Giclus10.04 Installation Procedure (PDF File)

• GIC Cluster Presentation

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

• Ms. Karla Miller's lecture presentations

Pattern Recognition

• My scripts

• Weka How Tos

• Matrices de confusión y otros valores estadísticos

• LIBSVM - A library for Support Vector Machines

• Spider SVM

• 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.

Working Diaries

Pedradas de Alex

Seguimientos