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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>LORIS - A Database System</title>
<!-- 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">
<!-- MNI ecosystem menu/summary-->
<section>
<!--<section>
<table class="reveal">
<tr>
<td width="60%" style="vertical-align: middle">
<a href="CBRAIN_indepth.html#/cbrain-indepth-destination"><img src = "images/cbrain-blue.png" style="border: 0; border-radius:30px;"></a>
</td>
<td width = "40%" style = "vertical-align: middle">
<a href="LORIS_indepth.html#/loris-indepth-destination"><img src = "images/loris-new-white.png" style="border: 0"></a>
</td>
</tr></table>
<h1> THE MNI ECOSYSTEM</h1>
<table class = "reveal">
<tr>
<td width = "25%" style = "vertical-align:middle">
<a href = "Brain_browser.html"><img src="images/BrainBrowser_SurfaceViewer.png"></a>
</td>
<td width = "25%" style = "vertical-align:middle">
<a href="Open_Science.html#/openscience-destination"><img src="images/Open_science.png"></a>
</td>
<td width = "25%" style = "vertical-align:middle">
<a href = "Big_brain.html"><img src="images/BigBrain.png"</a>
</td>
<td width = "25%" style = "vertical-align:middle">
<a href="Data_sharing.html#/data-sharing-destination"><img src="images/Data_sharing_cartoon.png"></a>
</td>
</tr></table>
</section>-->
<section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
</section>
<!-- MNI PAPER -->
<section data-transition="fade">
<a href="https://www.researchgate.net/publication/281780543_The_MNI_data-sharing_and_processing_ecosystem" target="_blank"><img src="images/MNI_ecosystem_paper.png"></a>
</section>
<section id="fragments">
<h2><font color="12a3d8">What’s involved?</font></h2>
<p>
<span class="fragment">Longitudinal Acquisition, Storage and Curation, </span>
<span class="fragment"><font color="f27c30">Interoperability, Reproducibility</font>, Transfer, Anonymization, </span>
<span class="fragment">Security, Privacy, Ethics, APIs, </span>
<span class="fragment">Validation, Quality Control, Protocol Checking, </span>
<span class="fragment">Preprocessing, Analysis, HPC, </span>
<span class="fragment">Provenance, Ontological Standarization, <font color="f27c30">Data Harmonization</font>, </span>
<span class="fragment">Upgrades, Maintenance, Bug Fixes, </span>
<span class="fragment">User Interface, Javascript, Bootstrap,</span>
<span class="fragment">Tracking, <font color="f27c30">Extensibility</font>, </span>
<span class="fragment">Data Management, Summary Statistics, </span>
<span class="fragment">Workflows, Development, Tool Integration, </span>
<span class="fragment"><font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>, </span>
<span class="fragment">Image Processing, Visualization, </span>
<span class="fragment">Networking, System Administration, </span>
<span class="fragment">Partnerships, Funding, HR</span>
<span class="fragment"><font color="f27c30">...No big deal!</font></span>
</p>
</section>
<section>
<h2><font color="12a3d8">LORIS-CBRAIN INTEGRATION</font></h2>
<p>Benefits <font color="f27c30">vs</font> Challenges</p>
<img src="images/Data_flow.jpg">
</section>
</section>
<!-- WHAT IS LORIS? -->
<section>
<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>
<a href="https://www.frontiersin.org/articles/10.3389/fninf.2011.00037/full" target="_blank"><img src="images/LORIS_paper.png"></a>
</td></tr></table>
</section>
<!-- PREFERRED SLIDE TO USE ON WHAT IS LORIS? -->
<section>
<a href="LORIS_indepth.html#/loris-indepth-destination" target="_blank"><h2>WHAT IS LORIS?</h2></a>
<table class="reveal" style="padding:0; margin:0">
<tr>
<td width="30%" style="vertical-align: middle">
<a href="http://loris.ca/" target="_blank"><img src="images/loris-new-white.png" style="border:0"></a>
</td>
<td width="70%" style="vertical-align: middle">
<p><small>“..is a modular and <font color="f27c30">extensible</font> web-based data and project management software for <font color="f27c30">neuroimaging research</font> studies. It is an <font color="f27c30">OPEN SOURCE</font> framework and database suitable for managing <font color="f27c30">large datasets</font>.”</small></p>
</td>
</tr></table>
<table class = "reveal" style="padding:0; margin:0" width="50%">
<tr>
<td width="30%" style="vertical-align:middle">
<h4 align="center"><font color="f27c30">Heterogenous data acquisition</font></h4>
</td>
<td width = "30%" style = "vertical-align:middle">
<center><img width="50%" src="images/right-arrow.png" style="background-color:#222222; border:0;"></center>
</td>
<td width = "30%" style="vertical-align:middle">
<h4 align="center"><font color="f27c30">Storage, processing & dissemination</font></h4>
</td>
</tr></table>
<img src="images/loris_versatility.png" align="center" width="90%" style="border:0">
<!-- <table class = "reveal" style="padding:0;margin:0" width = "60%">
<tr>
<td width="25%" style="vertical-align:middle">
<img src="images/multisite_study.png" style="border:0">
</td>
<td width="25%" style="vertical-align:middle">
<img src="images/longitudinal.png" style="border:0">
</td>
<td width="25%" style="vertical-align:middle">
<img src="images/clinical_research.png" style="border:0">
</td>
<td width="25%" style="vertical-align:middle">
<img src="images/public_dataset.png" style="border:0">
</td>
</tr></table> -->
</section>
<!-- WHAT DOES LORIS DO? -->
<section>
<h2>What does LORIS do?</h2>
<img src="images/LORIS_functionality.png">
</section>
<!-- PERFERRED SLIDE WHAT DOES LORIS DO -->
<section>
<h2>What does LORIS do?</h2>
<img src="images/loris_purpose.jpg" style="border:0" width="80%">
</section>
<!-- LORIS Key features -->
<section data-background="images/loris_features.jpg">
<!-- <h2><font color="0d4983">Key Features</font></h2>-->
</section>
<section>
<h2>Extensible and modular design</h2>
<table class="reveal">
<tr>
<td width="60%" style="vertical-align: middle">
<img src="images/Dashboard.png">
<img src="images/Imaging_scans.png">
</td>
<td width="40%" style="vertical-align: middle">
<img src="images/BrainBrowser_VolumeViewer.png">
<img src="images/Statistics_behavioural.png">
</td>
</tr>
</table>
</section>
<section data-background="images/LORIS_global_2.jpg" data-background-size="99%">
<h1 style="margin:350px 0px 0px 0px;"><font color ="0d4983">LORIS Globally</font></h1>
</section>
<!-- <section data-background="images/LORIS_full_functionality.png">
<h1><font color="blue">What does LORIS actually do?</font></h1>
</section> -->
<!-- PREFERRED SLIDE TO USE -->
<section>
<h2>What does LORIS actually do?</font></h2>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align:middle">
<h4 align="center"><font color="f27c30">
<span class="fragment">DATA ENTRY</span><br>
<span class="fragment">DATA MANAGEMENT</span><br>
<span class="fragment">DATA VISUALISATION</span><br>
<span class="fragment">DATA QUERYING</span><br>
</font></h4>
<h3 align="center"><a href="https://demo.loris.ca" target="_blank"><span class="fragment">TRY ME!</span></a></h3>
</td>
<td width="60%" style="vertical-align:middle">
<img src="images/loris_arch.png" style="padding:0; margin:0;">
</td>
</tr></table>
</section>
<!-- HETEROGENOUS DATA-->
<section data-background="images/LORIS_dashboard.png">
<h2><font color="222222">Heterogenous Data</font></h2>
<p><font color="f27c30">
<ul>
<span class="fragment"><li>Candidate Profile</li></span>
<span class="fragment"><li>Instrument Builder</li></span>
<span class="fragment"><li>Feedback Module</li></span>
<span class="fragment"><li>Double Data Entry</li></span>
<span class="fragment"><li>Conflict Resolver</li></span>
</ul>
</font></p>
</section>
<!-- IMAGING DATA -->
<section data-background="images/Imaging_scans_lego.png">
<h2 style="margin:-30px 0px 50px 0px;"><font color="0d4983">Imaging Data</font></h2>
<span class="fragment"><div style="background-color:white; border-radius:10px;"></span>
<p align="center" style="margin:0; padding:10px 0px 0px 0px;"><font color="f27c30">1. Acquisition & Storage</font></p>
<span class="fragment"><p align="center" style="margin:0; padding:0;"><font color="f27c30">2. Visualisation:</span><span class="fragment"> <font color="12a3d8">Imaging Browser,</span><span class="fragment"> BrainBrowser</font></font></p></span>
<span class="fragment"><p align="center" style="margin:0; padding:0px 0px 5px 0px;"><font color="f27c30">3. Quality Control:</span><span class="fragment"><font color="12a3d8"> Radiological Review Module,</span><span class="fragment"> DCC MRI</font></font></p></span>
</div>
</section
<!-- DQT & Sharing -->
<section data-background="images/Statistics_imaging_new.png">
<span class="fragment"><h2 style="margin:-220px 0px 200px 0px;"><font color="0d4983">Data Querying</font></h2></span>
<span class="fragment"><div align="left" style="margin:0px 200px 0px -50px; padding:0;"></span>
<ul><font color="f27c30">
<p align="center" style="margin:0; padding: 20px 0px 0px 0px;"><li>Imaging Statistiscs</li></p>
<span class="fragment"><p align="center" style="margin-bottom:-40px; padding: 0px 0px 20px 0px;"><li>Data Querying Tool <font color="12a3d8">(DQT)</font></li></p>
</font></ul></div>
</section>
<section data-background="images/DQT_Define_new.png" data-background-size="100%">
</section>
<section data-background="images/DQT_Results_new.png" data-background-size="100%">
</section>
<section data-background="images/DQT_Stats_new.png" data-background-size="100%">
</section>
<section data-background="images/Rogers_poster.PNG" data-background-size="70%">
<!--<h2><font color="222222">Module</font></h2>-->
</section>
<section data-background="images/Genomics_CNV.png">
</section>
</section>
<!-- WHAT IS LORIS? -->
<section id="loris-indepth-destination">
<section>
<h2>What can LORIS do (pointform)</h2>
<ul><small>
<li>Long Term Storage - Large datasets are valuable assets (e.g. ADNI)</li>
<li>Anonymity/Privacy - Ethics/IRB compliance and patient confidentiality</li>
<li>Data Sharing - Cross project collaborations</li>
<li>Secure Web Access- Available through a web browser</li>
<li>Heterogeneous Data Management - Single platform for MRI, PET, Clinical & Genetics data</li>
<li>Multimodal Data Querying - Easy querying of data, without requiring a programmer</li>
<li>Quality Control - Protocol violations, artefact detector, inter-rater reliability</li>
<li>Summary Statistics - Demographics, imaging, data entry</li>
<li>Processing Platform - Seamless serving of data to processing environments</li>
<li>Radiological Reviews - Visualization, including module to curate</li>
<li>Import/Export Capabilities - .xls, .csv, etc.</li>
<li>Biobanking - Tissue, blood and saliva samples</li>
<li>Visualization - 3D and 4D</li>
<li>Customizable & Extensible - New modules and features are possible</li>
<li>Open Source - Full access to source code. Code is free.</li>
</small></ul>
</section>
<!--STUDIES-->
<section data-transition="convex">
<a href="https://pediatricmri.nih.gov/nihpd/info/publications.html" target="_blank"><img src="images/NIHPD_logo.jpg"></a>
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<a href="http://www.sciencedirect.com/science/article/pii/S105381190500710X?via%3Dihub" target="_blank"><img src="images/NIHPD_paper.png"></a>
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/MRI_images_several.jpg">
</td>
<td width="30%" style="vertical-align: middle">
<p><small>
<ul>
<li>8 year study</li>
<li>Longitudinal data</li>
<li>532 subjects</li>
<li>8000 distinct variables</li>
<li>37000 individual assessments</li>
<li>T1, T2, PD, DTI</li>
<li>Spectroscopy</li>
<li>∼3TB of imaging data</li>
<li>2000 MRI acquisitions</li>
</ul>
</small></p>
</td>
</tr></table>
</section>
<section data-transition="convex">
<a href="http://www.ibis-network.org/" target="_blank"><img src="images/IBIS.png"></a>
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<a href="https://ajp.psychiatryonline.org/doi/abs/10.1176/appi.ajp.2011.11091447?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed" target="_blank"><img src="images/IBIS_paper.png"></a>
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/IBIS_image.png">
</td>
<td width="30%" style="vertical-align: middle">
<p><small>
<ul>
<li>Infant brain development in autism</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 of imaging data</li>
<li>Genetic/biospecimen data</li>
</ul>
</small></p>
</td>
</tr></table>
</section>
<!--CCNA-->
<section data-transition="convex">
<a href="http://ccna-ccnv.ca/en/" target="_blank"><img src="images/CCNA.png"></a>
</section>
<section>
<table class="reveal">
<a href="Big_brain.html target="_blank"><h2>BigBrain</h2></a>
<tr>
<td width="56%" style="vertical-align: middle">
<a href="https://bigbrain.loris.ca/main.php" target="_blank"><img src="images/BigBrain.png"></a>
</td>
<td width="44%" style="vertical-align: middle">
<a href="http://science.sciencemag.org/content/340/6139/1472" target="_blank"><img src="images/BigBrain_paper.png"></a>
</td>
</tr></table>
</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">
<a href="http://www.sciencedirect.com/science/article/pii/S1053811915003183" target="_blank"><img src="images/OMEGA.png"></a>
</td>
<td width="35%" style="vertical-align: middle">
<p><small>
<ul>
<li><a href="https://www.mcgill.ca/bic/resources/omega" target="_blank">Open MEG Archive</a></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>
<!-- MAVAN, Ludmer Centre -->
<section>
<table class="reveal">
<h2>MAVAN and the Ludmer Centre</h2>
<tr>
<td width="50%" style="vertical-align: middle">
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168812/" target="_blank"><img src="images/MAVAN_paper.png"></a>
</td>
<td width="50%" style="vertical-align: middle">
<p><small>
<ul>
<li>MAVAN</li><br>
<li>Maternal Adversity Vulnerability And NeuroDevelopement </li><br>
<li>Behavioral, Imaging and Genomics</li><br>
<li>Key project for the Ludmer Centre</li><br>
<li>Examining acute and chronic stressors on early childhood developement</li><br>
</ul>
</small></p>
</td>
</tr></table>
</section>
</section>
<!-- MNI Open Science -->
<section>
<section data-transition="convex">
<a href="Open_Science.html#/openscience-destination"><h2>Open Science</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<a href="http://www.sciencemag.org/news/2016/01/montreal-institute-going-open-accelerate-science" target="_blank"><img src="images/Open_science.png"></a>
</td>
<td width = "50%" style="vertical-align:middle">
<img width="85%" src="images/Nature_open_science.png">
</td></tr></table>
</section>
<section>
<img src="images/TOSI.png">
</section>
<section>
<h2>Open Science</h2>
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216036/" target="_blank"><img src="images/Open_science_paper.png" width="70%"></a>
</section>
<!--Cyberinfrastructure & Cybersecurity -->
<section>
<h2>Cyberinfrastructure</h2>
<img src="images/Cyberinfrastructure.png">
</section>
<section>
<h2>Open Science</h2>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<p><small>
<ul>
<li>Comprises the Biobank and Imaging Centre</li>
<li>LORIS is slated the platform for both</li>
<li>Data sharing at the MNI will be intergral to research</li>
<li>Designed to reduce duplication and make research more efficient</li>
</ul>
</small></p>
<p><small><font color="yellow">“We’re doing a really shitty job." -- Guy Rouleau </font></small></p>
</td>
<td>
<img src="images/Open_science.png">
</td></tr></table>
</section>
</section>
<!-- LORIS core -->
<section>
<section>
<h2>Login</h2>
<a href="https://demo.loris.ca" target="_blank"><img src="images/LORIS_login.png"></a>
</section>
<section>
<h2>Dashboard</h2>
<img src="images/Dashboard.png">
</section>
<section>
<h2>Summary Statistics</h2>
<img src="images/Statistics_behavioural.png">
</section>
<!-- LORIS SUMMARY STATISTICS -->
<section>
<h2>LORIS summary statistics</h2>
<img src="images/LORIS_numbers.png">
</section>
<section>
<h2>Permissions/User control</h2>
<img src="images/Permissions.png">
</section>
<section>
<h2>List of subjects</h2>
<img src="images/Subject_list.png">
</section>
<section>
<h2>Timepoints</h2>
<img src="images/Timepoint_list.png">
</section>
<section>
<h2>Battery of Measures</h2>
<p><small><font color="yellow">For list of 400+ instruments: <a href="https://sites.google.com/site/lorisinstrumentlist" target="_blank">https://sites.google.com/site/lorisinstrumentlist</a></font></small>
<img src="images/Battery.png">
</p>
</section>
<section>
<h2>Psychometric Subject Summary</h2>
<img src="images/AOSI.png">
</section>
<section>
<h2>Psychometric Data Entry</h2>
<img src="images/Psychometric2.png">
</section>
<section>
<h2>Survey Module</h2>
<img src="images/Survey_module.png">
</section>
</section>
<!-- Statistics
<section>
<section>
<h2>General Statistics</h2>
<img src="images/Statistics_general.png">
</section>
<section>
<h2>Imaging Statistics</h2>
<img src="images/Statistics_imaging.png">
</section>
</section>
-->
<!-- Imaging Browser -->
<section>
<section>
<h2>Imaging Browser</h2>
<img src="images/Imaging_menu.png">
</section>
<section>
<h2>Imaging Quality Control</h2>
<img src="images/Imaging_scans.png">
</section>
<section>
<a href = "images/Brain_browser.html" 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. <a href = "https://brainbrowser.cbrain.mcgill.ca/" target="_blank">TRY ME!</a></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>
<h3>BrainBrowser - <font color ="yellow"> 3D Surface Viewer </font></h3>
<p><a href="https://brainbrowser.cbrain.mcgill.ca/surface-viewer#ct" target="_blank"><img src="images/BrainBrowser_SurfaceViewer.png" width="80%"></a></p>
</section>
<section>
<h2><font color ="red">Protocol Violations</font></h2>
<img src="images/Violated_scans.png">
</section>
<section>
<table class="reveal">
<h2>Radiological Review Module</h2>
<tr>
<td width="61%" style="vertical-align: middle">
<img src="images/Radiological_review_menu.png">
</td>
<td width="39%" style="vertical-align: middle">
<img src="images/Radiological_review_form.png">
</td>
</tr></table>
</section>
<section>
<h2>DICOM archives</h2>
<img src="images/DICOM_archive.png">
</section>
<section>
<h2>Imaging Uploader -<font color="red"> New</font></h2>
<img src="images/Imaging_uploader.png">
</section>
<section>
<h2>Interactive Protocol Violations -<font color="red"> New</font></h2>
<img src="images/Violations.png">
</section>
<section>
<h2>Genomics Browser -<font color="red"> New</font></h2>
<img src="images/Imaging_uploader.png">
</section>
<section>
<h2>Improved Instrument Builder -<font color="red"> New</font></h2>
<img src="images/Imaging_uploader.png">
</section>
<section>
<h2>Configuration module -<font color="red"> New</font></h2>
<img src="images/Config.png">
</section>
<!-- LORIS Roadmap 2016 -->
<section>
<h2><font color="blue">LORIS Roadmap 2016</font></h2>
<p>
<p class="fragment roll-in">Easier Installation</p>
<p class="fragment roll-in">DQT integration and improvements</p>
<p class="fragment roll-in">API for imaging</p>
<p class="fragment roll-in">Imaging Browser Enhancements</p>
<p class="fragment roll-in">Documentation - help sections, wikis, code!</p>
<p class="fragment roll-in">Automated Testing</p>
<p class="fragment roll-in">Genomics</p>
<p class="fragment roll-in">QC modules</p>
<p class="fragment roll-in">Better stats</p>
<p class="fragment roll-in">Reduce rependencies - i.e. Quickforms</p>
</section>
</section>
<!-- Data Querying Tool -->
<section>
<section>
<h2>Data Dictionary Builder</h2>
<img src="images/Data_dictionary.png">
</section>
<section>
<h2>Data Querying Tool</h2>
<img src="images/DQT_Define.png">
</section>
<section>
<h2>Data Querying Tool - <font color="yellow"> Results</font></h2>
<img src="images/DQT_Results.png">
</section>
<section>
<h2>Data Querying Tool - <font color="yellow">Statistics</font></h2>
<img src="images/DQT_Stats.png">
</section>
</section>
<section>
<section>
<h2>Mobile <font color="yellow"> - Responsive layout</font></h2>
<img src="images/Mobile_responsive.png">
</section>
<section>
<h2>Mobile <font color="yellow"> - Data entry</font></h2>
<img src="images/Mobile_data_entry.png">
</section>
<section>
<h2>Mobile <font color="yellow"> - Imaging</font></h2>
<img src="images/Mobile_imaging.png">
</section>
</section>
<section>
<section>
<h2>LORIS - Github <font color="yellow"> - Open Source</font></h2>
<a href="https://github.com/aces/Loris" target="_blank"><p style="color: SteelBlue; line-height: 5px;"><small>https://github.com/aces/Loris</small></p></a>
<a href="https://github.com/aces/Loris" target="_blank"><img src="images/LORIS_Github.png" width="80%"></a>
</section>
<section>
<h2>LORIS - Github<font color="yellow"> Usage</font></h2>
<img src="images/github_usage2017.png">
</section>
<section>
<h2>LORIS - <font color="yellow">Requirements</font></h2>
<p class="fragment grow">Dedicated developer! (software is free of charge)</p>
<p class="fragment roll-in">LINUX based server</p>
<p class="fragment roll-in">LAMP stack</p>
<p class="fragment roll-in">Perl and other peripheral libraries (i.e DCMTK)</p>
<p class="fragment roll-in">Beer for Samir</p>
</section>
<section>
<h2>LORIS - <font color="yellow">Requirements for HBHL</font></h2>
<p class="fragment grow">Proper resourcing</p>
<p class="fragment roll-in">Reaslitic roadmap</p>
<p class="fragment roll-in">Create use cases</p>
<p class="fragment roll-in">Regular discussions</p>
<p class="fragment roll-in">Beer for Samir</p>
</section>
<section>
<h2>LORIS - <font color="blue"> Links</font></h2>
<p>Website: <a href="http:www.loris.ca" target="_blank"> www.loris.ca</a></p>
<p>Demo: <a href="https://demo.loris.ca" target="_blank"> https://demo.loris.ca</a></p>
<p>LORIS developers mailing list: <a href="mailto:loris-dev@bic.mni.mcgill.ca"> loris-dev@bic.mni.mcgill.ca</a></p>
<p>Source code: <a href="https://github.com/aces/Loris" target="_blank"> https://github.com/aces/Loris</a></p>
</section>
</section>
<!-- How can LORIS be useful for the MCIN? -->
<section>
<section>
<h2><font color="yellow">How can LORIS be useful to you?</font></h2>
</section>
<section>
<h2><font color="yellow">Testimonials</font></h2>
<p class="fragment roll-in">"You don't understand... LORIS saved our lives ... We could share our data anywhere. LORIS makes it really hard to share incorrect data. The quality control data is right there. You can share the QC... it's so well QCed"<font color="yellow"> -- Angelina Paolozza (NeuroDevenet, 2015)</font></p>
</section>
<section>
<h2><font color="yellow">Key Features for the lab</font></h2>
<p class="fragment roll-in">Organize your data</p>
<p class="fragment roll-in">Enable Quality Control</p>
<p class="fragment roll-in">Easy data sharing</p>
<p class="fragment roll-in">Provenance capture</p>
<p class="fragment roll-in">Facilitate image visualization</p>
<p class="fragment roll-in">Summary statistics</p>
<p class="fragment roll-in">Facilitate statistical analysis</p>
<p class="fragment roll-in">Linking your data across modalities</p>
<p class="fragment roll-in">Online Data Querying</p>
</section>
<section>
<h2><font color="yellow">Additional Features</font></h2>
<p class="fragment roll-in">Centralized data repository</p>
<p class="fragment roll-in">Download data from one place</p>
<p class="fragment roll-in">Centralized Document Repoistory</p>
<p class="fragment roll-in">Backup your data</p>
<p class="fragment roll-in">Consent is factored in</p>
<p class="fragment roll-in">Anonimyzed automatically online</p>
<p class="fragment roll-in">Raw data can be accessed (e.g. DICOM archiver)</p>
<p class="fragment roll-in">Tablet Friendly - Survey module</p>
</section>
<section>
<h2><font color="yellow">Data Sharing Initiatives</font></h2>
<p>
<p class="fragment roll-in">Public Data Repositories</p>
<p class="fragment roll-in">Collaborative Data releases</p>
<p class="fragment roll-in">CBRAIN hooks</p>
<p class="fragment roll-in">Ontologicial standardization (e.g. BIDS)</p>
<p class="fragment roll-in">External Provenance (e.g. NIDM)</p>
<p class="fragment roll-in">Interoperability with other competitors</p>
<p class="fragment roll-in">Open Science at the MNI</p>
</section>
<!-- Case example: CCNA -->
<section>
<table class="reveal">
<h2><a href ="https://docs.google.com/presentation/d/1y_4X5qaqYOfkdKvce4E5XJtG4BSxq0bG9M2-DrjijBs/edit#slide=id.p4">CCNA Case Example</a></h2>
<tr>
<td width="50%" style="vertical-align: middle">
<img src="images/CCNA.png">
</td>
<td width="50%" style="vertical-align: middle">
<p><small>
<ul>
<li>Canadian Consortium for Neurodegeration in Aging</li><br>
<li>Pan Canadian Study</li><br>
<li>$35 million study</li><br>
<li>More than 30 sites</li><br>
<li>Important project for this lab!</li><br>
</ul>
</small></p>
</td>
</tr></table>
</section>
</section>
<section>
<section>
<h2>Automated PET recognition</h2>
<img src="images/PET_GUI.png">
</section>
<section>
<h2>Automated PET recognition</h2>
<img src="images/PET_Github.png">
</section>
<section>
<h2>Enhanced DICOM anonymization</h2>
<ul>
<li>Going dcmtk free -- PYDICOM</li>
<li>CONDA</li>
<li>Satra knows everything!!</li>
</ul>
</section>
<section>
<h2>Enhanced DICOM anonymization</h2>
<img src="images/DICOM_Anon.png">
</section>
</section>
<!--<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<img width="50%" src="images/Royal_vic.png">
<h4>Acknowledgments</h4>
<p><small><font color="black">Alan Evans, Alex Zijdenbos, Reza Adalat, Penelope Kostopoulos, Louis Collins, Vladimir Fonov, Marc Rousseau, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Carolina Makowski, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Alden Woodward, Sylvain Milot, Jean Francois Malouin</font></small></p>
<p><small> <font color="white">LORIS Developers: </font><font color="black"> Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastien Muehlboeck, David Brownlee, Zia Mohades, David MacFarlane, Cecile Madjar, Mia Petkova, Christine Rogers, Rathi Gnanasekeran, Justin Kat, Nicolas Brossard, Tara Campbell, Jordan Stirling, Mouna Safi-Harab, Greg Luneau, Rida Abou-Haidar, Daniel Kroetz, Pierre-Emmaunel, Tom Beaudry, Shen Wang, John Saigle, Santiago Paiva, Xavier Lecours-Boucher, Stella Lee, Najmeh Khalili-Mahani, Sruthy Mathew, Zain Virani, Meaghan Evans, Liza Levitis, Angie Mosquera, Samira Haikel, Henri Rabalais & Zaliqa Rosli</font></small></p>
</section>-->
<!-- Acknowledgemnts -->
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
<tr>
<td width="70%" style="vertical-align: top">
<img src="images/loris_team_2017.jpg" width="90%">
</td>
<td width="30%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Acknowledgements:</font><font color="black" size="2"> Alan Evans, 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></p>
</td>
</tr></table>
</section>
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