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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Open Science & LORIS</title>
<meta name="description" content="A framework for easily creating beautiful presentations using HTML">
<meta name="author" content="Hakim El Hattab">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<!-- The important Javascript libraries -->
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/black.css" id="theme">
<!-- Code syntax highlighting -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? 'css/print/pdf.css' : 'css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<!-- Data Sharing -->
<section>
<section>
<h2>Open Science </h2>
<table class="reveal">
<tr>
<p><font color='yellow'>LORIS, EEG-BIDS, Git-Annex</font></p>
<p><small>May 14th, 2018<br>
Samir Das - Associate Director of Research Software Development <br>
McGill Centre for Integrative Neuroscience<br> Montreal Neurological Institute <br>[email protected]</small></p>
</tr>
<tr>
<td width="40%" style="vertical-align: middle">
<img src="images/MCIN.png" style="border: 0">
</td>
<td width="15%" style="vertical-align: middle">
<img src="images/Neuro.png" style="border: 0">
</td>
<td width="35%" style="vertical-align: middle">
<img src="images/ludmer-new-white.png" style="border: 0">
</td>
</tr>
</table>
</section>
<section data-transition="convex">
<img src="images/Spock.png">
</section>
</section>
<!-- Data sharing and Open Science in General Terms (6 slides) -->
<section data-transition="zoom">
<!-- Big Data Curve-->
<section>
<img src="images/Big_data.png">
</section>
<!-- Neuroinformatics Scope-->
<section>
<img src="images/Neuroinformatics_scope.jpg" width="70%">
</section>
<!-- COBIDAS -->
<section data-transition="concave">
<h2>Best practices in Data Sharing</h2>
<table class="reveal">
<tr>
<td style="vertical-align:middle">
<small style="margin:0; padding:0;"><a href="http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1" target="_blank">Committee on Best Practices in Data Analysis and Sharing (COBIDAS)</a></small>
</td>
<td width="20%" style="vertical-align:middle">
<img src="images/nature_neuro.jpg" style="border:0; margin:0; padding:0;">
</td>
</tr></table>
<table class="reveal">
<tr>
<td width="52%" style="vertical-align:middle">
<img src="images/COBIDAS.png">
</td>
<td width="48%" style="vertical-align:middle">
<img src="images/COBIDAS_Nature.png">
</td>
</tr></table>
</section>
<!-- Free as in beer-->
<section data-transition="zoom">
<a href="https://www.ohbmbrainmappingblog.com/blog/free-beer-and-free-speech-a-conversation-with-samir-das-and-pierre-bellec" target="_blank"><img src="images/Free_beer.png"></a>
</section>
<!-- Stallman -->
<section data-transition="concave">
<table class="reveal">
<tr>
<td width="50%" style="vertical-align:middle">
<img src="images/Stallman.png">
<p align="center">Richard Stallman <br>Visit to the MNI<br> May 2017</p>
</td>
<td width="50%" style="vertical-align:middle">
<img <img src="images/fsf_screenshot.png">
<img src="images/Stallman_Samir.png">
</td>
</tr></table>
</section>
</section>
<!-- MNI Open Science (4 Slides) -->
<section data-transition="concave">
<!-- Open Science Nature/Science articles -->
<section>
<h2>Open (Free) Science</h2>
<table class="reveal">
<tr>
<td width="47%" style="vertical-align: middle">
<img src="images/Nature_open_science.png">
</td>
<td width="53%" style="vertical-align:middle">
<img src="images/Open_science.png">
</td></tr></table>
</section>
<!-- TOSI -->
<section>
<img src="images/TOSI.png">
</section>
<!-- Open Science Cyberinfrastructure paper -->
<section>
<img src="images/Open_science_paper.png">
</section>
<section>
<h2>Cyberinfrastructure</h2>
<img src="images/Cyberinfrastructure.png">
</section>
</section>
<!-- Changes needed to make this reality -->
<section>
<h2>Specific Compnonents of Open Science</h2>
</section>
<!-- LORIS (5 slides) -->
<section data-transition="fade">
<section>
<a href="http://loris.ca/" target="_blank"><h2>WHAT IS LORIS?</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<a href="http://loris.ca/" target="_blank"><img src="images/loris-new-white.png"></a>
<p><small> “LORIS is a modular and <font color="f27c30">extensible</font> web-based data management system that integrates all aspects of a <font color="f27c30">multi-center</font> study: from <font color="f27c30">heterogeneous data acquisition</font> (imaging, clinical, behavior, genetics) to storage, <font color="f27c30">processing</font> and ultimately <font color="f27c30">dissemination</font>.”</small></p>
</td>
<td>
<img src="images/LORIS_paper.png">
</td></tr></table>
</section>
<!-- LORIS globally -->
<section data-background="images/LORIS_global.png">
</section>
<!-- LORIS Key features -->
<section data-background="images/LORIS_full_functionality.png">
<h2><font color="blue">LORIS Functionality</font></h2>
</section>
<!-- LORIS Dashboard -->
<section data-background="images/LORIS_dashboard.png">
<h2><font color="222222">LORIS Dashboard</font></h2>
</section>
<!-- IMAGING DATA -->
<section data-background="images/Imaging_scans_lego.png">
<h2 style="margin:-160px 0px 50px 0px;"><font color="00AABB">Imaging Data</font></h2>
</section>
<!-- Data Querying Interface -->
<section data-background="images/DQT_Define_new.png" data-background-size="100%">
<h2 style="margin:30px 0px 50px 0px;"><font color="0d4983">Cross-modal querying</font></h2>
</section>
<!-- Data Querying Results -->
<section data-background="images/DQT_Results_new.png" data-background-size="100%">
<h2><font color="222222">Real-time Query Results</font></h2>
</section>
<section data-background="images/Genomics_CNV.png">
<h2 style="margin: 5px 0px 0px 0px;"><font color="222222">Genomics Browser</font></h2>
</section>
<!-- GITHUB -->
<section>
<img src="images/LORIS_github_new.png">
</section>
</section>
<!-- BIDS -->
<section>
<section data-transition="fade" data-background="images/BIDS.png">
</section>
<!-- BIDS -->
<section data-transition="fade">
<table class="reveal">
<h2>BIDS Format</h2>
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/BIDS_paper.png">
</td>
<td width="55%" style="vertical-align: middle">
<img src="images/BIDS_structure.png">
</td>
</tr></table>
</section>
<!-- EEG BIDS -->
<section data-transition="fade">
<img src="images/BIDS_EEG.png">
</section>
</section>
<!-- Git Annex -->
<section data-transition="fade">
<img src="images/Git_annex.png">
</section>
<!-- Centralized versus De-centralized -->
<section data-transition="concave">
<h2>Centralized or Distributed?</h2>
<img src="images/Networks.png" width="80%">
</section>
<!-- Acknowledgemnts and Open Science Beers at Else's-->
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
<tr>
<td width="60%" style="vertical-align: top">
<img src="images/loris_team_new.jpg">
</td>
<td width="40%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Special thanks to Pierre Bellec... for being so geeky. :)</font><font color="black" size="2">... and Cecile Madjar</font></small></p>
<p><font color="blue" size="4">LORIS team on left</font> <font size="2" color="black"></p>
</td>
</tr></table>
</section>
<!-- Infrastructure (8 Slides)-->
<section>
<section>
<h2>Improved Infrastructure</h2>
<p> Databases, NoSQL, APIs, Version Control, Provenance Capture</p>
</section>
<section>
<h2>NoSQL</h2>
<img src="images/NoSQL_database.jpg">
</section>
<section>
<h2>LORIS API</h2>
<p align="center"><font color="12a3d8">Instrument Format</font></p>
<img width="80%" src="images/LORIS_api.png">
</section>
<!-- NeuroImgaging Data Model (NiDM)-->
<section data-transition="fade">
<table class="reveal">
<h2>NeuroImaging Data Model</h2>
<tr>
<td width="55%" style="vertical-align: middle">
<img src="images/Nidm.png">
</td>
<td width="45%" style="vertical-align: middle">
<img src="images/NIDM_paper.png">
</td>
</tr></table>
</section>
</section>
<!-- Standarization -->
<section data-transition="convex">
<!-- APIs -->
<section data-background="images/Solutions.png">
<h2><font color="black">API Building and Standardization</font></h2>
</section>
<!-- Easily available data (9 Slides)-->
<section data-transition="zoom">
<section>
<h2>Consolidated datasets</h2>
<p>
<span class="fragment"><a href="http://adni.loni.usc.edu" target="_blank">ADNI, </a>
<a href="http://www.loni.usc.edu/ICBM/" target="_blank">ICBM, </a>
<a href="http://pediatricmri.nih.gov/nihpd/info/index.html" target="_blank">NIHPD, </a>
<a href="http://mouse.brain-map.org" target="_blank">Allen Mouse Brain, </a>
<a href="https://ndar.nih.gov/edit_collection.html?id=19" target="_blank">IBIS, </a>
<a href="http://www.generationr.nl/researchers.html" target="_blank">Generation-R, </a>
<a href="http://fcon_1000.projects.nitrc.org/indi/abide/" target="_blank">ABIDE, </a>
<a href="http://preprocessed-connectomes-project.org/abide/" target="_blank">ABIDE Preprocessed, </a>
<a href="http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html" target="_blank">ADHD 200, </a>
<a href="http://neurobureau.projects.nitrc.org/ADHD200/Introduction.html" target="_blank">ADHD Preprocessed, </a>
<a href="http://www.humanconnectomeproject.org" target="_blank">Human Connectome Project, </a>
<a href="https://omega.bic.mni.mcgill.ca/main.php" target="_blank">OMEGA, </a>
<a href="http://www.ukbiobank.ac.uk" target="_blank">UK Biobank, </a></span>
<span class="fragment"><a href="" target="_blank">Edinburgh Biobank, </a>
<a href="https://bigbrain.loris.ca/main.php" target="_blank">BigBrain, </a>
<a href="http://www.talairach.org" target="_blank">Talairach, </a>
<a href="http://fcon_1000.projects.nitrc.org/indi/enhanced/" target="_blank">1000 Functional Connectomes, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27" target="_blank">Colin 27, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" target="_blank">MNI 305, </a>
<a href="http://journal.frontiersin.org/article/10.3389/fnagi.2014.00149/full" target="_blank">1000 Brains, </a>
<a href="http://qnl.bu.edu/obart/explore/AAL/" target="_blank">AAL, </a>
<a href="" target="_blank">ANIMAL, </a>
<a href="" target="_blank">MAVAN, </a>
<a href="http://www.preventad.com" target="_blank">PreventAD, </a>
<a href="http://pingstudy.ucsd.edu" target="_blank">PING, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" target="_blank">MNI 152, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" target="_blank">MNI 305, </a></span>
<span class="fragment"><a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/" target="_blank">FSL... </a></span>
</p>
<p><b><font color="green"><span class="fragment">Not </span></font>
<font color="yellow"><span class="fragment">enough </span></font></b>
<font color="red"><span class="fragment">datasets! </span></font>
</p>
</section>
<!-- BigBrain -->
<section data-transition="fade">
<table class="reveal">
<h2>BigBrain</h2>
<tr>
<td width="55%" style="vertical-align: middle">
<img src="images/BigBrain.png">
</td>
<td width="45%" style="vertical-align: middle">
<img src="images/BigBrain_paper.png">
</td>
</tr></table>
</section>
<section>
<img src="images/bigbrain_data.png">
</section>
<!-- ADNI -->
<section data-transition="zoom">
<h2>ADNI</h2>
<table class="reveal">
<tr>
<td style="vertical-align: middle">
<img src="images/ADNI_paper.png">
</td>
<td style="vertical-align: top">
<p>
<ul>
<li>Cited 343 times</li><br>
<li>Data-use agreements</li><br>
<li>Used for countless analyses</li><br>
<li>Restrictive</li><br>
</ul>
</p>
</td>
</tr></table>
</section>
<!-- NIHPD -->
<section data-transition="convex">
<img src="images/NIHPD_logo.jpg">
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/NIHPD_paper.png">
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/MRI_images_several.jpg">
</td>
<td width="30%" style="vertical-align: top">
<ul><small>
<li>Cited 295 times</li>
<li>Control data for NDAR</li>
<li>Longitudinal study (8 years)</li>
<li>532 subjects</li>
<li>8000 distinct variables</li>
<li>37000 individual assessments</li>
<li>T1, T2, PD, DTI, Spectroscopy</li>
<li>∼3TB of imaging data</li>
<li>2000 MRI acquisitions</li>
</small></ul>
</td>
</tr></table>
</section>
<!-- IBIS -->
<section data-transition="convex">
<img src="images/IBIS.png">
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/IBIS_paper.png">
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/IBIS_image.png">
</td>
<td width="30%" style="vertical-align: top">
<p><small>
<ul>
<li>Autism infant brain development</li>
<li>3000+ scans</li>
<li>700+ subjects</li>
<li>7000 distinct variables</li>
<li>150,000+ individual assessments</li>
<li>T1, T2, DTI, BOLD</li>
<li>∼5 TBs imaging data</li>
<li>Genetic/biospecimen data</li>
</ul>
</small></p>
</td>
</tr></table>
</section>
<!-- CCNA -->
<section data-transition="concave">
<table class="reveal">
<h2>CCNA</h2>
<tr>
<td width="70%" style="vertical-align: top">
<img src="images/CCNA.png">
</td>
<td width="30%" style="vertical-align: top">
<p><small>
<ul>
<li>$35 million</li><br>
<li>CIHR funded</li><br>
<li>Pan Canadian Consortium</li><br>
<li>Acquisition in June, 2016</li><br>
<li>35 collections sites</li><br>
<li>LORIS powered</li><br>
</ul>
</small></p>
</td>
</tr></table>
</section>
<!-- ABIDE -->
<section data-transition="fade">
<table class="reveal">
<h2>ABIDE</h2>
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/ABIDE_paper.png">
</td>
<td width="55%" style="vertical-align: middle">
<img src="images/ABIDE_preprocessed.png">
</td>
</tr></table>
</section>
<!-- QPN -->
<section data-transition="fade">
<h2>Quebec Parkinson Network</h2>
<img src="images/QPN.png" width="80%">
</section>
<!-- OMEGA - small pilot, interest has spiked -->
<section data-transition="convex">
<table class="reveal">
<h2><a href="https://omega.bic.mni.mcgill.ca">OMEGA</a></h2>
<tr>
<td width="65%" style="vertical-align: middle">
<img src="images/OMEGA.png">
</td>
<td width="35%" style="vertical-align: middle">
<p><small>
<ul>
<li>Open MEG Archive</li><br>
<li>First open MEG repository</li><br>
<li>180 user accounts created</li><br>
<li>Associated structural data</li><br>
<li>500+ reads on academia.edu</li><br>
</ul>
</small></p>
</td>
</tr></table>
</section>
</section>
<!-- Tools (7 Slides) -->
<section data-transition="slide">
<!-- List of Tools -->
<section data-transition="convex">
<h2>Tools and Environments</h2>
<p>
<span class="fragment"><a href="https://www.incf.org" target="_blank">Neurovault, </a>
<a href="https://osf.io" target="_blank">NeuroSynth, </a>
<a href="https://www.nitrc.org" target="_blank">CIVET, </a>
<a href="http://alleninstitute.org" target="_blank">VIP, </a>
<a href="https://ndar.nih.gov" target="_blank">Boutiques, </a>
<a href="https://openfmri.org" target="_blank">Git-Annex, </a>
<a href="http://www.humanbrainmapping.org" target="_blank">SOLID, </a>
<a href="https://www.humanbrainproject.eu" target="_blank">BIDS, </a>
<a href="https://www.computecanada.ca" target="_blank">NiDM, </a>
<a href="https://www.maelstrom-research.org" target="_blank">DiCAT, </a>
<a href="http://www.ukbiobank.ac.uk" target="_blank">DCMTK, </a>
<a href="http://nipy.org/nipype/" target="_blank">NiPype, </a>
<a href="http://www.braininitiative.nih.gov" target="_blank">ITK, </a>
<a href="http://enigma.ini.usc.edu" target="_blank">Freesurfer, </a></span>
<span class="fragment"><a href="http://fcon_1000.projects.nitrc.org/indi/enhanced/" target="_blank">SPM, </a>
<a href="http://www.loni.usc.edu" target="_blank">FSL, </a>
<a href="http://" target="_blank">Mobile MRI, </a>
<a href="http://coins.mrn.org" target="_blank">1000 Brains, </a>
<a href="http://www.xnat.org" target="_blank">AAL, </a>
<a href="https://www.braincode.ca" target="_blank">BrainCode, </a>
<a href="https:" target="_blank">GitHub, </a>
<a href="https://aws.amazon.com" target="_blank">Amazon Cloud, </a>
<a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/" target="_blank">FSL, </a>
<a href="https://ida.loni.usc.edu" target="_blank">IDA, </a>
<a href="http://brainvisa.info" target="_blank">BrainVisa, </a>
<a href="https://cmind.research.cchmc.org" target="_blank">DICOM Confidential, </a>
<a href="https://cmind.research.cchmc.org" target="_blank">DockerHub, </a>
<a href="http://www.opengatecollaboration.org" target="_blank">Gate, </a>
<a href="https://cmind.research.cchmc.org" target="_blank">CMIND... </a></span>
</p>
<p><b><font color="green"><span class="fragment">Too </span></font>
<font color="yellow"><span class="fragment">many </span></font></b>
<font color="red"><span class="fragment">Tools! </span></font>
</section>
<!-- Neurovault -->
<section data-transition="fade">
<img src="images/Neurovault.png">
</section>
<section data-transition="fade">
<h2>Neurovault Example</h2>
<img src="images/Neurovault_example.png">
</section>
<!-- NeuroSynth-->
<section data-transition="fade">
<img src="images/NeuroSynth.png" width=90%">
</section>
<!-- BrainBrowser -->
<section>
<a href = "https://brainbrowser.cbrain.mcgill.ca" target="_blank"><h2>BrainBrowser</h2></a>
<p>..a set of web-based <font color="f27c30"><b>3D visualization tools</b></font> primarily used for viewing <font color="12a3d8">neurological data</font> i.e. <font color="12a3d8">MRI scans</font>.</p>
<p><small>It allows for real-time <font color="f27c30">manipulation</font> and <font color="f27c30">analysis</font> of 3D neuroimaging data through any modern web browser.</small></p>
<table class = "reveal">
<tr>
<td width="40%" vertical-align:middle">
<img src="images/BrainBrowser_VolumeViewer.png">
</td>
<td width="60%" vertical-align:middle">
<img src="images/BrainBrowser_SurfaceViewer.png">
</td>
</tr></table>
</section>
</section>
<!-- Data Publishing -->
<section>
<section data-transition="fade" data-background="images/data_publishing.png">
<h1 style="margin:-100px 0px 0px 0px;"><font color="purple">Data Publishing</font></h1>
<h1 style="margin: 0px 0px 50px 0px:"><font color="purple">Not Data Sharing</font></h1>
</section>
<!-- EU going Open Access -->
<section data-transition="fade">
<img src="images/Open_access.png">
</section>
<!-- Faculty 1000 -->
<section data-transition="fade">
<img src="images/F1000.png">
</section>
<!-- FAIR -->
<section data-transition="fade">
<img src="images/FAIR.png">
</section>
<section data-transition="fade">
<h2>Data Publishing Geeksquad for Persistent DOIs</h2>
<img src="images/Data_publishing_geeks.jpg">
</section>
</section>
<!-- Brainhack -->
<section data-transition="fade">
<table class="reveal">
<h2><a href="">Hackathons</a></h2>
<tr>
<td width="75%" style="vertical-align: middle">
<img src="images/C-BASE.png">
</td>
<td width="25%" style="vertical-align: middle">
<p> Important value of hackathons to data sharing initiatives</p>
<img src="images/Brainhack.png">
</td>
</tr></table>
</section>
<!-- MNI ecosystem -->
<section>
<section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
</section>
<section data-background="images/MNI_ecosystem_paper.png" data-transition="fade" data-background-size="70%">
</section>
<section id="fragments">
<h2><font color="12a3d8">What’s involved?</font></h2>
<p>
<span class="fragment">Longitudinal Acquisition, Storage and Curation,
<font color="f27c30">Interoperability</font>, Reproducibility, Transfer, Anonymization,
Security, Privacy, Ethics, APIs,
Validation, Quality Control, Protocol Checking,
Preprocessing, Analysis, HPC, </span>
<span class="fragment">Provenance, Ontological Standarization, <font color="f27c30">Data Harmonization</font>,
Upgrades, Maintenance, Bug Fixes,
User Interface, Javascript, Bootstrap,
Tracking, <font color="f27c30">Extensibility</font>,
Data Management, Summary Statistics,
Workflows, Development, Tool Integration, </span>
<span class="fragment"><font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>,
Image Processing, Visualization,
Networking, System Administration,
Partnerships, Funding, HR bureaucracies</span>
<span class="fragment"><font color="f27c30">...No big deal!</font></span>
</p>
</section>
<section>
<h2><font color="12a3d8">Data flow</font></h2>
<img src="images/Data_flow.jpg">
</section>
</section>
<!-- LORIS (5 slides) -->
<section data-transition="fade">
<section>
<a href="http://loris.ca/" target="_blank"><h2>WHAT IS LORIS?</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<a href="http://loris.ca/" target="_blank"><img src="images/loris-new-white.png"></a>
<p><small> “LORIS is a modular and <font color="f27c30">extensible</font> web-based data management system that integrates all aspects of a <font color="f27c30">multi-center</font> study: from <font color="f27c30">heterogeneous data acquisition</font> (imaging, clinical, behavior, genetics) to storage, <font color="f27c30">processing</font> and ultimately <font color="f27c30">dissemination</font>.”</small></p>
</td>
<td>
<img src="images/LORIS_paper.png">
</td></tr></table>
</section>
<!-- LORIS globally -->
<section data-background="images/LORIS_global.jpg" data-background-size="99%">
<!--<h1><font color ="blue">LORIS globally</font></h1> -->
</section>
<!-- LORIS Key features -->
<section data-background="images/loris_features.jpg">
<!--<h2><font color="0d4983">Key Features</font></h2>-->
</section>
<!-- LORIS Dashboard -->
<section data-background="images/LORIS_dashboard.png">
<h2><font color="222222">LORIS Dashboard</font></h2>
</section>
<!-- IMAGING DATA -->
<section data-background="images/Imaging_scans_lego.png">
<h2 style="margin:-160px 0px 50px 0px;"><font color="00AABB">Imaging Data</font></h2>
</section>
<!-- Data Querying Interface -->
<section data-background="images/DQT_Define_new.png" data-background-size="100%">
<h2 style="margin:30px 0px 50px 0px;"><font color="0d4983">Cross-modal querying</font></h2>
</section>
<!-- Data Querying Results -->
<section data-background="images/DQT_Results_new.png" data-background-size="100%">
<h2><font color="222222">Real-time Query Results</font></h2>
</section>
<section data-background="images/Genomics_CNV.png">
<h2 style="margin: 5px 0px 0px 0px;"><font color="222222">Genomics Browser</font></h2>
</section>
</section>
<!-- CBRAIN (7 slides)-->
<section>
<section>
<table class="reveal">
<h2><a href="http://www.cbrain.ca">CBRAIN</a></h2>
<tr>
<td width="50%" style="vertical-align: top">
<p><small><font color="yellow">Several default tools:</font>
<ul>
<li>CIVET</li>
<li>CivetCombiner</li>
<li>CivetQC</li>
<li>Freesurfer</li>
<li>SPM-batch</li>
<li>NIAK</li>
<li>FSL (bedpostx, bet, fast, feat, first flirt, melodic, probtrackx)</li>
<li>Numerous converters</li>
<li>And many more...</li>
</ul>
<p><a href="mailto:[email protected]">[email protected]</a></p>
</td>
<td width="50%" style="vertical-align: middle">
<img src="images/CBRAIN_paper.png" width="80%">
</td>
</tr></table>
</section>
<!--CBRAIN portal-->
<section data-transition="convex">
<h2>CBRAIN projects</h2>
<a href="https://portal.cbrain.mcgill.ca/login" target="_blank"><img src="images/CBRAIN_mainpage.png"></a>
<a href="https://portal.cbrain.mcgill.ca/login" target="_blank"><h4><font color="12a3d8">TRY ME!</font></h4></a>
</section>
<!-- CBRAIN TASKS-->
<section data-background="images/CBRAIN_tasks.png" data-background-size="85%">
</section>
<!-- WHO USES CBRAIN?-->
<section data-background="images/CBRAIN_distribution.png" data-background-size="70%">
<span class="fragment"><h2><font color="12a3d8">NOW</font></h2></span>
<p><font color="0d4983"><span class="fragment">611 users; </span><span class="fragment">199 international</span><br>
<span class="fragment">191 sites</span><br>
<span class="fragment">299 countries</span></font></p>
</section>
<!--CBRAIN SCHEMA-->
<section data-background="images/CBRAIN_arch.png" data-background-size="70%">
<!--<h2>CBRAIN SCHEMA</h2>
<img src="images/CBRAIN_arch.png" width="80%">-->
</section>
<!-- CIVET (and NIAK?) -->
<section data-background="images/CIVET_processing_steps.png" data-background-size="70%">
<img src="images/CIVET_logo.png" align="right" width="15%">
</section>
<section>
<h2>NIAK</h2>
<img src="images/NIAK.jpg" width="80%">
</section>
</section>
<!-- MNI Open Science -->
<section data-transition="convex">
<!-- Challenges and Hurdles -->
<section>
<h2><font color="yellow">Challenges and Hurdles</font></h2>
<table>
<thead>
<tr>
<th><font color="yellow"> </font></th>
<th><font color="yellow"> </font></th>
</tr>
</thead>
<tbody>
<tr>
<td>Future unknowns</td>
<td>Fear of getting scooped</td>
</tr>
<tr>
<td>Waste/duplication</td>
<td>Technical challenges</td>
</tr>
<tr>
<td>Decreased exposure</td>
<td>Privacy concerns</td>
</tr>
<tr>
<td>Changing the Publishing Culture</td>
<td>Data Harmonization</td>
</tr>
<tr>
<td>Licensing and legal aspects</td>
<td>Interoperability</td>
</tr>
<tr>
<td>More attrition</td>
<td>Reproducibility</td>
</tr>
<tr>
<td>Sustainibility</td>
<td>Obtaining ethics</td>
</tr>
<tr>
<td>Funding</td>
<td>Scalability</td>
</tr>
</tbody>
</table>
</section>
<!-- Problem Case -->
<section data-transition="convex">
<h2>Privacy Concerns</h2>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align: middle">
<img src="images/Data_breach_title.png">
<img src="images/Data_breach_consent.png">
<img src="images/Data_breach.png">
</td>
<td width="60%" style="vertical-align: middle">
<a href="https://tech.vijayp.ca/of-taxis-and-rainbows-f6bc289679a1#.jbat052vf"><img src="images/Data_breach_NYC_taxi.png"></a>
<small><a href="https://www.mcgill.ca/bic/channels/event/feindel-brain-imaging-lecture-series-adrian-thorogood-embracing-open-science-best-practices-258420" target="_blank">Adrian Thorogood BIC lecture - March 9, 2016</a></small>
<img src="images/Data_breach_magazine.png">
</td>
</tr></table>
</section>
<!-- Cybersecurity -->
<section>
<img src="images/Cybersecurity.png">
</section>
<!-- Other concerns -->
<section data-transition="fade">
<h2>Buy-in from other researchers!</h2>
</section>
</section>
<!-- Open Science socials -->
<section>
<h2> Open Science Beers </h2>
<p> Beers at Else's - Wednesday's at 4:44pm</p>
<img src="images/beer_oclock.png">
</section>
<!-- Acknowledgemnts and Open Science Beers at Else's-->
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
<tr>
<td width="60%" style="vertical-align: top">
<img src="images/loris_team_new.jpg">
</td>
<td width="40%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Acknowledgements:</font><font color="black" size="2"> Alex Zijdenbos, Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, Reza Adalat, Louis Collins, Vladimir Fonov, Marc Rousseau, Mia Petkova, Rathi Gnanasekaran, David Brownlee, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Najma Mahani, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin, Sylvain Baillet, Daniel Kroetz, Martin Weiss, Mathieu Desrosier, Jason Karamchandani, Amit Bar-Or, Ted Fon, John Brietner, Derek Lo, Patrick Bermudez, Chris Steele, Pamela Patterson and one of my favourites: Pierre Bellec!</font></small></p>
<p><font color="blue" size="4">LORIS team on left</font> <font size="2" color="black"><br>Special thanks to Alan Evans for making all of this possible.</font></p>
</td>
</tr></table>
</section>
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