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Línea 1: Línea 1:
== Oier Echaniz Beneitez ==
"Ever tried. Ever failed. No matter. Try Again. Fail again. Fail better." - Samuel Beckett
<br/>
"Solving a problem in a hundred years is, practically speaking, the same as not solving it at all." - Steven Pinker


<h3>Personal Data</h3>
{{Infobox
|name        =
|bodystyle    =
 
|titlestyle  =
|abovestyle = background:#cfc;
|subheaderstyle =
|title        = My info
|above        = Oier Echaniz
|subheader    = PhD Student/Researcher/PDI
|subheader2  =
 
|imagestyle  =
|captionstyle =
|  image      = [[File:Oier2.jpg|350px|alt=Myself, right now]]
|caption      =  Myself, Right now


* <b>E-mail: </b>oier.echaniz@ehu.es
|headerstyle  = background:#ccf;
|labelstyle  = background:#ddf;
|datastyle    =


* <b>Address:</b>
|header1 = Personal Data
:Computational Intelligence Group
| label1 =
|  data1 =
|header2 =
| label2 = E-mail
|  data2 = oier.echaniz@ehu.eus
|header3 =
| label3 = Twitter
|  data3 = [https://twitter.com/oiertwo oiertwo]
|header4 =
| label4 = LinkedIn
|  data4 = [https://es.linkedin.com/in/oier-echaniz-93887a38 Oier Echaniz]
|header5 =
| label5 = Zenodo contrib.
|  data5 = [https://zenodo.org/search?page=1&size=20&q=%22Oier%20Echaniz%22 Oier Echaniz]
|header6 =
| label6 = Tlfn
|  data6 = (+34) 943.01.80.47
|header7 = Address
| label7 =
|  data7 =
|header8 =
| label8 =
|  data8 = :Computational Intelligence Group
:Department of Computer Science and Artificial Intelligence
:Department of Computer Science and Artificial Intelligence
:Computer Science Faculty - Lab. 307
:Computer Science Faculty - '''Lab. 307'''
:University Of The Basque Country (UPV/EHU)  
:University Of The Basque Country (UPV/EHU)  
:Paseo Manuel Lardizabal 1 - CP: 20018 Donostia/San Sebastián (GUIPUZCOA) - Spain
:Paseo Manuel Lardizabal 1 - CP: 20018 Donostia/San Sebastián (GUIPUZCOA) - Spain


* <b>Tfno.:</b> (+34) 943.01.80.47
|belowstyle = background:#ddf;
|below      =
}}
 
 
== Oier Echaniz Beneitez ==
 
[[File:Ezgif-com-crop.gif|frame|Radiofrequency Image]]
 
"Ever tried. Ever failed. No matter. Try Again. Fail again. Fail better." - Samuel Beckett
<br/>
"Solving a problem in a hundred years is, practically speaking, the same as not solving it at all." - Steven Pinker
<br/>


<h3>
<h3>
Línea 24: Línea 71:
* [http://www.kisa.ehu.es/ Masters Degree in Computational Engineering and Intelligent Systems] (2012/2013) - Universidad del País Vasco (UPV/EHU).
* [http://www.kisa.ehu.es/ Masters Degree in Computational Engineering and Intelligent Systems] (2012/2013) - Universidad del País Vasco (UPV/EHU).
* Currently:  
* Currently:  
: PhD Student in the [http://www.ehu.es/ccwintco/ Computational Intelligence Group] of the Computer Science and Artificial Intelligence Department - Universidad del País Vasco (UPV/EHU).
: Researcher (PDI) at the [http://www.ehu.es/ccwintco/ Computational Intelligence Group] of the Computer Science and Artificial Intelligence Department - Universidad del País Vasco (UPV/EHU).


<br/>
<br/>
Línea 34: Línea 81:
* June/2011 - March/2012 - Research assistant at '''Tecnalia Research and Innovation'''  
* June/2011 - March/2012 - Research assistant at '''Tecnalia Research and Innovation'''  
:Data mining and optimization algorithms used to predict errors in a aeronautic production.
:Data mining and optimization algorithms used to predict errors in a aeronautic production.
* January/2013 - December/2015 - CTO/Founder at '''Asmatu Intelligent Solutions'''
:Optimization and machine learning for industry


<br/>
<br/>
== Software ==
* [https://github.com/oiertwo/vampyr Vampyr]: a Python module to analysis statistically blood samples.
* [https://github.com/oiertwo My github homepage]
* [https://github.com/neurita Neurita free software packages]
* [https://asmatzen.wordpress.com/ Asmatzen] (my blog)
== Publications ==


<h3>
<h3>
2015
Organizations and volunteering
</h3>
</h3>
* [http://www.pyss.org Python San Sebastian Society] - Chair (since 2014)
* [http://www.europython-society.org/members EuroPython Society]
** Member (since 2015).
** Board of directors (2015-2017)
** Media WG member (2017 - now)
* [http://pyss.org/euskopython/ EuskoPython Society] - Chair (since 2014)
* European Network for the Study of Cholangiocarcinoma ([http://www.enscca.org ENS-CCA]) - supporting member
* [http://www.aspanogi.org/index.php/es/ Aspanogi] - Volunteer/Helper (since 2014)
* [http://www.pyjok.es PyJokes] Society - Spokesperson and contributor
* [http://software-carpentry.org/ Software Carpentry]  - Instructor


<br/>
<br/>


== Projects ==
== Software ==


*Entreprenari Saria 2012
* [https://github.com/oiertwo/vampyr Vampyr]: a Python module to analize statistically blood samples.


<br/>
* [https://github.com/oiertwo My github homepage]


== Organizer ==
* [https://github.com/neurita Neurita free software packages]


* Local organizing committee member of Europython 2015 ([http://ep2015.europython.eu/ Europython 2015])
* [https://asmatzen.wordpress.com/ Asmatzen] (my blog)
* Local organizing committee member of Python San Sebastian 2014 ([http://www.pyss.org Pyss14])


== Research Areas ==
* [https://github.com/pyjokes PyJokes FOSS packages]
* Pattern recognition applied to medical images
* Medical image processing


<br/>
* [https://zenodo.org/record/2580383 BIOTHINGS]: a Python library to create bio-related pipelines


== Pending Tasks ==
<br>
* ITK, ANTS...
* OpenMP and MPI
* Multivariate Analysis
* [https://www.nmr.mgh.harvard.edu/~lazar/ Meditate]
* DTI modeling
* Process Ann's DTI dataset
* Add MRI and ML related info pages with literature reviews on this wiki.


<br/>
== Datasets ==


== Conferences ==
* Radiomics:
- CSV ready for data analysis. Features extracted with PyRadiomics after preprocessing Head and Neck image database.  [https://zenodo.org/record/3660998#.XkFJbOEo-q4 Download at Zenodo] ( Doi: 10.5281/zenodo.3660998 )


== Publications ==


<br/>
<h3>
Accepted
</h3>




<br/>
<h3>
2019
</h3>




=== Databases ===
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Carlos M Chiesa-Estomba, '''Oier Echaniz''', Ekhiñe Larruscain, Jose A Gonzalez-García, Jon A Sistiaga-Suarez, Manuel Graña
: Radiomics and Texture Analysis in Laryngeal Cancer. Looking for new frontiers in precision medicine thought Imaging analysis.
: Cancers
: DOI: 10.3390/cancers11101409 / JCR 2018 6.162 (Q1 Oncology)
</div>


BRAIN IMAGES
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Oier Echaniz''', Manuel Graña
: BIOTHINGS: A Pipeline Creation Tool for PAR-CLIP Sequence Analsys
: 8th INTERNATIONAL WORK-CONFERENCEON THE INTERPLAY BETWEEN NATURALAND ARTIFICIAL COMPUTATION (IWINAC 2019)
: DOI: 10.1007/978-3-030-19591-5_34
</div>


* [http://www.oasis-brains.org OASIS]


* [http://fcon_1000.projects.nitrc.org/index.html INDI - 1000 Functional Connectomes Project]
<h3>
2018
</h3>


* [http://adni.loni.ucla.edu/ ADNI]
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Oier Echaniz''', Manuel Graña
: A Comparison of PAR-CLIP Peak Calling Approaches on Noisy Data
: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
: DOI: 10.1109/BIBM.2018.8621210
</div>


* [http://www.nitrc.org/projects/brainmap BrainMap]
<h3>
2017
</h3>


* [http://rad.med.hokudai.ac.jp/research/fa/index_e.php Fractional Anisotropy Database]
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Marta Fernandez-Mercado, Erika Larrea, Izaskun Ceberio, Ibai Goicoechea, '''Oier Etxaniz''', Julien Buratti, Yufei Luo, Marcos Arauzo-Bravo,Markus Landthaler, Charles H. Lawrie1
: NOVEL TARGET GENES OF DEREGULATED MIRNAS IN DLBCL REVEALED BY ENDOGENOUS AGO2 PAR-CLIP
: 22nd Congress of the European Hematology Association (E-POSTER)
</div>


* [http://insight-journal.org/midas MIDAS]
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Manuel Grana, '''Oier Echaniz''', Beatriz Rodriguez-Vigil and Idoia Labayen.
: Automated segmentation of visceral adiposity in MRI in obese children
: CORES 2017
</div>


* [http://www.childmind.org/en/healthy-brain-network/abide/ ABIDE]
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Oier Echaniz''', Manuel Graña
: Ongoing work on deep learning for lung cancer prediction"
: IWINAC 2017
</div>


* [http://fcon_1000.projects.nitrc.org/indi/retro/cobre.html COBRE-Schizophrenia]
<h3>
2016
</h3>


PROSTATE
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Manuel Graña, '''Oier Echaniz'''
: Views on Electronic Health Record
: Inmed 2016
</div>


OTHER
<h3>
 
2015
=== Research Groups ===
</h3>
 
* [http://www.fmrib.ox.ac.uk/ Oxford Centre for Functional MRI of the Brain] - University of Oxford - JR Hospital - England
 
* [http://cmic.cs.ucl.ac.uk Centre of Medical Image Computing] - University College London - Gower Street - Eng. Building
 
* [http://dbm.neuro.uni-jena.de Structural Brain Mapping Group] - University of Jena - Thüringen - central Germany
 
* [https://www.rad.upenn.edu/sbia/software/index.html Section of Biomedical Image Analysis] - University of Pennsylvania
 
* [http://www.mpih-frankfurt.mpg.de Max Planck Institute für Hirnforschung]
 
* [http://image.hggm.es/ Laboratorio de Imagen Médica. Unidad de Medicina y Cirugía Experimental] - Hospital General Universitario Gregorio Marañón
 
* [http://www2.bic.mni.mcgill.ca/ McConnell Brain Imaging Centre (BIC) of the Montreal Neurological Institute (MNI)] - McGill University
 
* [http://www.na-mic.org/ National Alliance for Medical Image Computing]
 
* [http://www-sop.inria.fr/asclepios/ Asclepios project] - INRIA Sophia-Antipolis
 
* [http://www-sop.inria.fr/odyssee/en/ ODYSSEE research project-team] - INRIA Sophia-Antipolis
 
* [http://www.mr.ethz.ch/ Divisions of Bioimaging and MRI Technology] - University and ETH Zurich
 
* [http://www.bigr.nl/website/ Biomedical Imaging Group Rotterdam] - Erasmus MC - University Medical Center Rotterdam


* [http://mindhive.mit.edu/ A community portal for MIT brain research] - Massachussets Institute of Technology
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Medrano M, Maiz E, Maldonado-Martín S, Arenaza L, Rodríguez-Vigil B, Ortega FB, Ruiz JR, Larrarte E, Díez I, Sarasúa A, Tobalina I, Barrenechea L, Pérez-Asenjo J, Kannengiesser S, Manhães-Savio A, '''Echaniz O''', Labayen I
: The effect of a multidisciplinary intervention program on hepatic adiposity in overweight-obese children: protocol of the EFIGRO study
: Contemporary Clinical Trials
: DOI: 10.1016/j.cct.2015.09.017
</div>


* [http://www.siani.es Instituto Universitario de Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería] - ULPGC
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Oier Echaniz''', Borja Ayerdi, Alexandre Savio, Manuel Graña
: An Ad-Hoc Image Segmentation of Subcutaneous and Visceral Adipose Tissue from Abdomino-Pelvic Magnetic Resonance Images
: Inmed 2015
</div>


* [http://www.fei.edu.br/~cet/ipl.html Image Processing Lab de la FEI] Sao Bernardo do Campo (SP) - Brasil
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Borja Ayerdi, '''Oier Echaniz''', Alexandre Savio, Manuel Graña
: Automated Segmentation of Subcutaneous and Visceral Adipose Tissues from MRI
: Inmed 2015
</div>


<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Alexandre Savio, '''Oier Echaniz''', Manuel Graña
: Comparando Cerebros con la Morfometría Basada en Voxel Clave: P
: Semana del cerebro, San Sebastián, 9/03/2015 (POSTER)
</div>
<br/>
<br/>


== Utilities ==
== Editorships ==


=== Scientific Writing ===
<h3>
2018
</h3>
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Editors: Graña, M., López-Guede, J.M., '''Etxaniz, O.''', Herrero, Á., Sáez, J.A., Quintián, H., Corchado, E. (Eds.)
: International Joint Conference SOCO’18-CISIS’18-ICEUTE’18
: ISBN 978-3-319-94120-2 [https://www.springer.com/us/book/9783319941196 link]
</div>


* [[Media:How_to_write_a_good_introduction.pdf | Chapter "How to Write an Introduction" of Professor Glasman-Deal's Science Research Writing For Non-Native Speakers of English]] ( [http://www.worldscibooks.com/general/p605.html Ref.] )


* [[Media:Writing_about_methodology.pdf | Chapter "Writing about methodology" of Professor Glasman-Deal's Science Research Writing For Non-Native Speakers of English]]
<h3>
2016
</h3>
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
Editors: Graña, M., López-Guede, J.M., '''Etxaniz, O.''', Herrero, Á., Sáez, J.A., Quintián, H., Corchado, E. (Eds.)
: International Joint Conference SOCO’16-CISIS’16-ICEUTE’16
: ISBN 978-3-319-94120-2 [https://www.springer.com/gp/book/9783319473635 link]
</div>


* [[Media:Customize_and_improve_matlab_plots.pdf | Customise and improve Matlab plots.]]
== Recognitions ==
<h3>
2017
</h3>
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Medalla al merito ciudadano:'''
ASPANOGI, San Sebastian, 2017
: As part of Aspanogi volunteering team.
: [http://www.eitb.eus/es/noticias/sociedad/detalle/4586845/donostia-dara-20-enero-2017-medallas-al-merito-ciudadano/ link]
</div>


=== Computer Settings ===
<h3>
2016
</h3>


* [[como-instalar-vpn-en-ubuntu | Install Cisco VPN client on Ubuntu 8.04]]
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Acknowledgement at:''' <br>
Jesus M Banales et al.
: Expert consensus document: Cholangiocarcinoma: current knowledge and future perspectives consensus statement from the European Network for the Study of Cholangiocarcinoma (ENS-CCA)
: Nature Reviews Gastroenterology & Hepatology
: doi:10.1038/nrgastro.2016.51
: [http://www.nature.com/nrgastro/journal/vaop/ncurrent/full/nrgastro.2016.51.html#acknowledgments link]
</div>


* [[SPIE LaTEX manuscript templates and writing guidelines]]
<h3>
2012
</h3>
<div style="border:1px solid #CCC; background-color: #FCFCFC; padding: .5em; font-size: 85%; margin: 1em auto 1 em 0; width: 80%">
'''Entreprenari saria 2012:''' <br>
Best end of grade project with business projections.
</div>


* [http://www.cs.stir.ac.uk/~kjt/software/latex/showbst.html BibTeX Style Examples]
== Activities ==


* [http://impressive.sourceforge.net Impressive - The stylish way of giving PDF presentations]
[[File:Pink-car.jpg|thumb|frame|350px| Borja & I, Wroclaw, 2015]]


* Install ITK and Kitware software from sources. [http://www.itk.org/Wiki/ITK_Configuring_and_Building] [http://www.vtk.org/Wiki/Complete_Setup] (for more information ask me)
(x) future events, find me in this activities!


* [http://www.itk.org/Wiki/ITK_Python_Wrapping Install python wrapper on building ITK from sources.]
<h3>Lecturer/Speaker</h3>
* Instructor of Software Carpentry Workshop at Lund University 2016 ([https://alexsavio.github.io/2016-05-25-lunduni/ LundSWC])
* Speaker and workshop instructor of European Maker Week Gasteiz 2016 ([http://events.europeanmakerweek.eu/events/view/127 makerday])


* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation#Types_of_Slicer_3_Plugins Create a 3DSlicer Plugin]
<h3>Organization</h3>


* [http://davyd.livejournal.com/230629.html Sync Tomboy Notes]
'''2020'''


* [[Pushing_references_from_JabRef_To_Lyx | Push references from JabRef to Lyx]]
* [CANCELED TO 2021] Local organizing comittee and Co-chair of the conference of EuroScipy 2020 Bilbao ([https://www.euroscipy.org/2020/ EUROSCIPY 2020])
* [CANCELED TO 2021] Local organizing comittee of GeoPython 2020 Bilbao ([http://2020.geopython.net/ GeoPython 2020])
* [POSTPONED TO LATER 2020] Organizing committee member of HacKCancer Datathon 2020


* [http://neuro.debian.net/ Página de instalación de FSL en Debian]
'''2019'''
* Local organizing comittee and Co-chair of the conference of EuroScipy 2019 Bilbao ([https://www.euroscipy.org/2019/ EUROSCIPY 2019])
'''2018'''
* Local organizing committee member of Python San Sebastian 2018 ([http://pyss18.pyss.org Pyss16])
* Local organizing committee and Co-Chair of organizing committee of ICEUTE 2018 ([http://www.ehu.eus/ccwintco/iceute2018/ ICEUTE 2018])
* Local organizing committee and Co-Chair of organizing committee of SOCO 2018 ([http://www.ehu.eus/ccwintco/iceute2018/ SOCO 2018])
* Local organizing committee and Co-Chair of organizing committee of CISIS 2018 ([http://www.ehu.eus/ccwintco/iceute2018/ CISIS 2018])
* Organizing committee member of HacKCancer Datathon 2018 ([http://www.hackcancer.eu Hackcancer])
'''2017'''
* Local organizing committee member of Python San Sebastian 2017 ([http://pyss17.pyss.org Pyss17])
* Organizing committee as Board Member of Europython 2017 ([https://ep2017.europython.eu Europython 2017])
'''2016'''
* Local organizing committee member of Python San Sebastian 2016 ([http://pyss16.pyss.org Pyss16])
* Local organizing committee member of ICEUTE 2016 ([http://www.ehu.eus/ccwintco/iceute2016/ ICEUTE 2016])
* Local organizing committee member of SOCO 2016 ([http://www.ehu.eus/ccwintco/soco2016/ SOCO 2016])
* Local organizing committee member of CISIS 2016 ([http://www.ehu.eus/ccwintco/cisis2016/ CISIS 2016])
* Local organizing committee member of Europython 2016 ([http://ep2016.europython.eu/ Europython 2016])
* Local organizing committee and helper of Software Carpentry Workshop CFM-EHU 2016
* Local organizing committee member of the I International Monothematic Congress in Cholangiocarcinoma ([http://conf2016.enscca.org MCCCA])
'''2015'''
* Local organizing committee member of Python San Sebastian 2015 ([http://pyss15.pyss.org Pyss15])
* Local organizing committee (Host) and helper of Software Carpentry Workshop CFM-EHU 2015
* Local organizing committee member of Europython 2015 ([http://ep2015.europython.eu/ Europython 2015])
* Local organizing committee member of Python San Sebastian 2014 ([http://pyss14.pyss.org Pyss14])


* [[Setting up FSL to use a SunGridEngine or computing cluster]]
<br>


* [[How to install Springer LNCS Style for Lyx]]
<h3> Attendee </h3>
Attended conferences as participant
* (Invited but not Attended due to collapse and covid-19 date change) Retos de futuro en la medicina 2020 - Madrid, Spain. Invitados junto a Manuel Graña y Carlos Chiesa. ([https://www.fundacionmercksalud.com organizado e invitado por merc salud])
* IWINAC 2017 - La Coruña, Galicia, Spain
* CORES 2017 - Polanica-Zdroj, Poland
* Inmed 2016 - Tenerife, Canary Islands, Spain
* PyconSette - Florence, Italy
* Inmed 2015 - Tokyo, Japan
* CORES 2015 - Wroclaw, Poland
* Big Data meets Machine Learning 2015 - Wroclaw, Poland
* EuroPython 2014 - Berlin, Germany


* [http://www.oak-tree.us/blog/index.php/2009/12/02/latex-cv-part3#more-1332 Automatically Generate a List of Publications for your CV]
<br>


* [http://www.ehu.es/ccwintco/files/giclus_installation_procedure_technical_note.html Setting up a Ubuntu 10.04.1 cluster (NFS, NIS, Sun Grid Engine, FSL)] [[Media:Giclus_installation_procedure_technical_note.pdf | Giclus10.04 Installation Procedure (PDF File)]]
== SUBPAGES ==


* [[Media:Giclus_sun_grid_engine-2010.pdf | GIC Cluster Presentation]]
# [[Usuario:Oier.echaniz/interes|Interesting links and projects]]
# [[Usuario:Oier.echaniz/media|Media appearances]]


* [[Media:Git for dummies.png | Git Cheat sheet for Dummies.]]
== Research Areas ==
* Pattern recognition applied to medical images
* Medical image processing
* Radiomics
* Omics


=== Image Processing ===
<br/>


* [[Nomenclatura_planos_de_corte | Nomenclatura de los planos de corte en los seres vivos]]
== Pending Tasks ==
* Save the world


* [http://www.na-mic.org/svn/NAMICSandBox/trunk/ NA-MIC Software Repository]
<br/>
 
* [http://www.imagemagick.org/Usage ImageMagick Usage Examples]
 
* [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html FSL VBM How to]
 
* [http://www.nitrc.org/projects/multimodereg BRAINSFit - Rigid Registration Tool]
 
* [[Statistical Parametric Mapping]]
 
* [http://en.wikibooks.org/wiki/SPM/Programming_intro SPM Programming Intro]
 
* [http://www.sph.umich.edu/~nichols/JohnsGems5.html SPM5-Specific code snippets by John Ashburner]
 
* [http://www.ogre3d.org/wiki/index.php/Quaternion_and_Rotation_Primer#Quaternion_Rotations A Quaternion and Rotation Primer]
 
* [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html FMRIB's Diffusion Toolbox - FDT v2.0]


* [http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training 3D Slicer User Documentation]
== Leisure Time ==
"We are here on Earth to fart around, and don't let anybody tell you different." - Kurt Vonnegut


* [http://www.sph.sc.edu/comd/rorden/workshop/fsl/dti/index.html Short introduction to DTI analysis]
* [http://www.akondiatik.com Ordago] movie Codirector (Canceled)
 
* [http://www.nitrc.org/projects/art/ Automatic Registration Toolbox (ART)]
 
* [http://www.ogre3d.org/wiki/index.php/Quaternion_and_Rotation_Primer#Quaternion_Rotations A Quaternion and Rotation Primer]
 
* [http://www.picsl.upenn.edu/ANTS/ Advanced Open Source Tools for Normalization and Neuroanatomy (SyN nonlinear registration algorithm)]
 
* [http://www.itksnap.org Semi-Automatic and Manual Segmentation of 3D Volumes]
 
* [http://www.parallelpython.com Parallel Python for parallel processing]
 
* [http://www.cs.ucl.ac.uk/staff/g.ridgway/masking/ Mask creation software for VBM analyses for SPM8]
 
* [http://afni.nimh.nih.gov/afni/community/board/read.php?f=1&i=2066&t=1278&v=f Preprocessing steps for SPM Analyze images to use them on FSL]
 
* [http://www.fmrimethods.org/index.php/Main_Page fMRI methods]
 
* [http://www.fmrib.ox.ac.uk/Members/karla/lectures-and-teaching-material Ms. Karla Miller's lecture presentations]
 
* [[media:fdt.pdf | FMRIB Diffusion Toolbox]]
 
=== Pattern Recognition ===
 
* [[alexsavio_scripts | My scripts]]
 
* [[Wiki Weka | Weka How Tos]]
 
* [[Matrices de confusión y otros valores estadísticos]]
 
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM - A library for Support Vector Machines]
 
* [http://www.support-vector-machines.org/SVM_soft.html Spider SVM]
 
* [http://www.vias.org/tmdatanaleng/cc_scaling.html Teach Me Data Analysis (Range scaling)]
 
* [http://page.mi.fu-berlin.de/rojas/neural/index.html.html Neural Networks - A Systematic Introduction]
 
* [[Presentaciones-informes-software-veganzones | Some interesting presentations]]
 
* [http://www.siam.org/meetings/op08/invited.php Invited speakers for SIAM Conference on Optimization] (Modersitzki presentation on image registration)
 
=== Real World ===
 
* [[Media:Useful things to know about the PhD.pdf | Some useful hints to know about the PhD]]
 
* [http://www.youtube.com/watch?v=XViCOAu6UC0 What the Simpsons think about graduate students!!]
 
* [[Media:InsightOpenScience.pdf | Presentación de Luis Ibañez sobre el sin sentido del entorno de "ciencia abierta" en la que trabajamos.]] ( [http://www.kitware.com/company/team/ibanez.html Página personal de Luis Ibañez en Kitware] )
 
* [https://www-304.ibm.com/jct09002c/university/scholars/collaborativeresearch/results.html Collaborative Research Initiatives]
 
* [[Media:OpenCollaborationPrinciples_2005.pdf | Principios de colaboración abierta en la investigación (2005)]]
 
* [http://boloniaiifordummies.blogspot.com/2008/11/preguntas-y-respuestas.html Preguntas y respuestas sobre la situación Ingeniería Informática - Tratado de Bolonia, con referencias.]
 
* [http://www.acceleratingfuture.com/michael/works/tenreasons.htm 10 Reasons]
 
* [http://www.ehu.es/ccwintco/index.php/Usuario:Natafresa#Visita_al_Instituto_Nacional_de_Pesquisas_Espaciais_.28INPE.29.2C_Sao_Jos.C3.A9_Dos_Campos_.28Brasil.29.2C_Enero_2009 Visita al Instituto Nacional de Pesquisas Espaciais (INPE), Sao José Dos Campos (Brasil), Enero 2009]
 
* [[fotos-veganzones | Miguel's Photo gallery]]
 
<br/>

Revisión actual - 02:21 24 mar 2020

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Oier Echaniz Beneitez

Radiofrequency Image

"Ever tried. Ever failed. No matter. Try Again. Fail again. Fail better." - Samuel Beckett
"Solving a problem in a hundred years is, practically speaking, the same as not solving it at all." - Steven Pinker

Studies

Researcher (PDI) at the Computational Intelligence Group of the Computer Science and Artificial Intelligence Department - Universidad del País Vasco (UPV/EHU).


Work Experience

  • June/2011 - March/2012 - Research assistant at Tecnalia Research and Innovation
Data mining and optimization algorithms used to predict errors in a aeronautic production.
  • January/2013 - December/2015 - CTO/Founder at Asmatu Intelligent Solutions
Optimization and machine learning for industry


Organizations and volunteering


Software

  • Vampyr: a Python module to analize statistically blood samples.
  • BIOTHINGS: a Python library to create bio-related pipelines


Datasets

  • Radiomics:
- CSV ready for data analysis. Features extracted with PyRadiomics after preprocessing Head and Neck image database.  Download at Zenodo ( Doi: 10.5281/zenodo.3660998 )

Publications

Accepted


2019


Carlos M Chiesa-Estomba, Oier Echaniz, Ekhiñe Larruscain, Jose A Gonzalez-García, Jon A Sistiaga-Suarez, Manuel Graña

Radiomics and Texture Analysis in Laryngeal Cancer. Looking for new frontiers in precision medicine thought Imaging analysis.
Cancers
DOI: 10.3390/cancers11101409 / JCR 2018 6.162 (Q1 Oncology)

Oier Echaniz, Manuel Graña

BIOTHINGS: A Pipeline Creation Tool for PAR-CLIP Sequence Analsys
8th INTERNATIONAL WORK-CONFERENCEON THE INTERPLAY BETWEEN NATURALAND ARTIFICIAL COMPUTATION (IWINAC 2019)
DOI: 10.1007/978-3-030-19591-5_34


2018

Oier Echaniz, Manuel Graña

A Comparison of PAR-CLIP Peak Calling Approaches on Noisy Data
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
DOI: 10.1109/BIBM.2018.8621210

2017

Marta Fernandez-Mercado, Erika Larrea, Izaskun Ceberio, Ibai Goicoechea, Oier Etxaniz, Julien Buratti, Yufei Luo, Marcos Arauzo-Bravo,Markus Landthaler, Charles H. Lawrie1

NOVEL TARGET GENES OF DEREGULATED MIRNAS IN DLBCL REVEALED BY ENDOGENOUS AGO2 PAR-CLIP
22nd Congress of the European Hematology Association (E-POSTER)

Manuel Grana, Oier Echaniz, Beatriz Rodriguez-Vigil and Idoia Labayen.

Automated segmentation of visceral adiposity in MRI in obese children
CORES 2017

Oier Echaniz, Manuel Graña

Ongoing work on deep learning for lung cancer prediction"
IWINAC 2017

2016

Manuel Graña, Oier Echaniz

Views on Electronic Health Record
Inmed 2016

2015

Medrano M, Maiz E, Maldonado-Martín S, Arenaza L, Rodríguez-Vigil B, Ortega FB, Ruiz JR, Larrarte E, Díez I, Sarasúa A, Tobalina I, Barrenechea L, Pérez-Asenjo J, Kannengiesser S, Manhães-Savio A, Echaniz O, Labayen I

The effect of a multidisciplinary intervention program on hepatic adiposity in overweight-obese children: protocol of the EFIGRO study
Contemporary Clinical Trials
DOI: 10.1016/j.cct.2015.09.017

Oier Echaniz, Borja Ayerdi, Alexandre Savio, Manuel Graña

An Ad-Hoc Image Segmentation of Subcutaneous and Visceral Adipose Tissue from Abdomino-Pelvic Magnetic Resonance Images
Inmed 2015

Borja Ayerdi, Oier Echaniz, Alexandre Savio, Manuel Graña

Automated Segmentation of Subcutaneous and Visceral Adipose Tissues from MRI
Inmed 2015

Alexandre Savio, Oier Echaniz, Manuel Graña

Comparando Cerebros con la Morfometría Basada en Voxel Clave: P
Semana del cerebro, San Sebastián, 9/03/2015 (POSTER)


Editorships

2018

Editors: Graña, M., López-Guede, J.M., Etxaniz, O., Herrero, Á., Sáez, J.A., Quintián, H., Corchado, E. (Eds.)

International Joint Conference SOCO’18-CISIS’18-ICEUTE’18
ISBN 978-3-319-94120-2 link


2016

Editors: Graña, M., López-Guede, J.M., Etxaniz, O., Herrero, Á., Sáez, J.A., Quintián, H., Corchado, E. (Eds.)

International Joint Conference SOCO’16-CISIS’16-ICEUTE’16
ISBN 978-3-319-94120-2 link

Recognitions

2017

Medalla al merito ciudadano: ASPANOGI, San Sebastian, 2017

As part of Aspanogi volunteering team.
link

2016

Acknowledgement at:
Jesus M Banales et al.

Expert consensus document: Cholangiocarcinoma: current knowledge and future perspectives consensus statement from the European Network for the Study of Cholangiocarcinoma (ENS-CCA)
Nature Reviews Gastroenterology & Hepatology
doi:10.1038/nrgastro.2016.51
link

2012

Entreprenari saria 2012:
Best end of grade project with business projections.

Activities

Borja & I, Wroclaw, 2015

(x) future events, find me in this activities!

Lecturer/Speaker

  • Instructor of Software Carpentry Workshop at Lund University 2016 (LundSWC)
  • Speaker and workshop instructor of European Maker Week Gasteiz 2016 (makerday)

Organization

2020

  • [CANCELED TO 2021] Local organizing comittee and Co-chair of the conference of EuroScipy 2020 Bilbao (EUROSCIPY 2020)
  • [CANCELED TO 2021] Local organizing comittee of GeoPython 2020 Bilbao (GeoPython 2020)
  • [POSTPONED TO LATER 2020] Organizing committee member of HacKCancer Datathon 2020

2019

  • Local organizing comittee and Co-chair of the conference of EuroScipy 2019 Bilbao (EUROSCIPY 2019)

2018

  • Local organizing committee member of Python San Sebastian 2018 (Pyss16)
  • Local organizing committee and Co-Chair of organizing committee of ICEUTE 2018 (ICEUTE 2018)
  • Local organizing committee and Co-Chair of organizing committee of SOCO 2018 (SOCO 2018)
  • Local organizing committee and Co-Chair of organizing committee of CISIS 2018 (CISIS 2018)
  • Organizing committee member of HacKCancer Datathon 2018 (Hackcancer)

2017

  • Local organizing committee member of Python San Sebastian 2017 (Pyss17)
  • Organizing committee as Board Member of Europython 2017 (Europython 2017)

2016

  • Local organizing committee member of Python San Sebastian 2016 (Pyss16)
  • Local organizing committee member of ICEUTE 2016 (ICEUTE 2016)
  • Local organizing committee member of SOCO 2016 (SOCO 2016)
  • Local organizing committee member of CISIS 2016 (CISIS 2016)
  • Local organizing committee member of Europython 2016 (Europython 2016)
  • Local organizing committee and helper of Software Carpentry Workshop CFM-EHU 2016
  • Local organizing committee member of the I International Monothematic Congress in Cholangiocarcinoma (MCCCA)

2015

  • Local organizing committee member of Python San Sebastian 2015 (Pyss15)
  • Local organizing committee (Host) and helper of Software Carpentry Workshop CFM-EHU 2015
  • Local organizing committee member of Europython 2015 (Europython 2015)
  • Local organizing committee member of Python San Sebastian 2014 (Pyss14)


Attendee

Attended conferences as participant

  • (Invited but not Attended due to collapse and covid-19 date change) Retos de futuro en la medicina 2020 - Madrid, Spain. Invitados junto a Manuel Graña y Carlos Chiesa. (organizado e invitado por merc salud)
  • IWINAC 2017 - La Coruña, Galicia, Spain
  • CORES 2017 - Polanica-Zdroj, Poland
  • Inmed 2016 - Tenerife, Canary Islands, Spain
  • PyconSette - Florence, Italy
  • Inmed 2015 - Tokyo, Japan
  • CORES 2015 - Wroclaw, Poland
  • Big Data meets Machine Learning 2015 - Wroclaw, Poland
  • EuroPython 2014 - Berlin, Germany


SUBPAGES

  1. Interesting links and projects
  2. Media appearances

Research Areas

  • Pattern recognition applied to medical images
  • Medical image processing
  • Radiomics
  • Omics


Pending Tasks

  • Save the world


Leisure Time

"We are here on Earth to fart around, and don't let anybody tell you different." - Kurt Vonnegut

  • Ordago movie Codirector (Canceled)
Obtenido de «http://ehu.eus/ccwintco/index.php?title=Usuario:Oier.echaniz&oldid=19778»