Usuario:Alexsavio

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Material

Seguimientos

Pedradas

Surveys (wiki under construction)

Alexandre Manhães Savio

Studies

• Information Engineer (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. Beca de Formación de Personal Investigador del Gobierno Vasco desde Enero del 2010, renovable los 3 años siguientes.

Work Experience

• February/2008 - December/2009 - Research assistant at the Computational Intelligence Group of the Computer Science and Artificial Intelligence department - University of the Basque Country

MR image processing and application of classification algorithms for the detection of brain neuronal disorders.

• 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

Post-processed datasets from the work done in the group.

2011

On Current Biomarkers for Alzheimer's Disease detected by Machine Learning techniques

A. Savio, A. Bourisly, M. Graña

ISMRM SCIENTIFIC WORKSHOP: Neuroimaging Biomarkers of Psychiatric Disorders: What are They?. 13-16 October 2011. Montabaur, Germany

• slides (PDF)
• slides (Prezi flash)

Computer Aided Diagnosis system for Alzheimer Disease using brain Diffusion Tensor Imaging features selected by Pearson's correlation.

M. Graña, M. Termenon, A. Savio, A. Gonzalez-Pinto, J. Echeveste, J. M. Pérez, A. Besga

Neuroscience Letters (recently accepted)

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

• draft

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 Chyzhyk, 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.

articulos de revistas en proceso de redacción

• TBM y Oasis
• DTI modelo 3

conferencias en el horno

• ISMRM workshop on Biomarkers en Montabaur

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 on 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

• IEEE Transactions on Biomedical Engineering

• Journal of MRI

• 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

• International Symposium on Biomedical Imaging

• 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

• AddNeuroMed

Research Groups

• Oxford Centre for Functional MRI of the Brain - University of Oxford - JR Hospital - England

• 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. )

• Chapter "Writing about methodology" of Professor Glasman-Deal's Science Research Writing For Non-Native Speakers of English

• Customise and improve Matlab plots.

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

• FMRIB Diffusion Toolbox

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