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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 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>
<!--CBRAIN-->
<section>
<section>
<a href="CBRAIN_indepth.html#/cbrain-indepth-destination" target="_blank"><h2>WHAT IS CBRAIN?</h2></a>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<a href="https://www.frontiersin.org/articles/10.3389/fninf.2014.00054/full" target="_blank"><img src="images/CBRAIN_paper.png" width="90%"></a>
</td>
<td width="50%" style="vertical-align: middle;">
<a href="https://mcin-cnim.ca/technology/cbrain/" target="_blank"><img src="images/cbrain-blue.png" style="border:0; border-radius:30px;"></a>
<p><small><br>“..is an <font color="12a3d8">OPEN SOURCE</font> web-based collaborative <font color="12a3d8">High-Performance Computing (HPC)</font> platform for <font color="12a3d8">neuroimaging research</font>, connecting researchers to the <font color="12a3d8">tools</font> required to handle <font color="12a3d8">large datasets</font>.”</small></p>
<!--<p align="center"><small><ol>
<span class="fragment"><li>Processing <font color="f27c30">data</font></li></span><br>
<span class="fragment"><li>Abstract complexities associated with using <font color="f27c30">HPC</font> resources for <font color="f27c30">image processing</font></li></span>
</ol></small></p>-->
</td>
</tr></table>
</section>
<!-- What does CBRAIN do? -->
<section data-background="images/NIAK.jpg">
<h2 style="background-color:white;border-radius:15px;margin:-70px 100px 50px 100px"><font color="12a3d8">What does CBRAIN do?</font></h2>
<span class="fragment"><p style="background-color:white; margin: 0px 30px -1000px 30px; border-radius:15px;"><b><font color="f27c30">..enables distributed execution of software pipelines</font></b></p></span>
</section>
<section data-background="images/cbrain_uniview.png">
<p style="background-color:white; padding:0; border-radius:15px;margin:-20px -50px 0px -50px;"><b><font color="12a3d8">..aggregates multiple distributed file systems into uniform view</font></b></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>
<!-- 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 Computing Resources-->
<section data-background="images/CBRAIN_hours.png" data-background-size="80%">
<span class="fragment"><h2 style="margin-top:-100px;"><font color="12a3d8">CBRAIN Computing Resources</font></h2></span>
<span class="fragment"><img src="images/cbrain_stats.png" align="left" width="60%" style="margin-top:100px;"></span>
</section>
<!--CBRAIN portal-->
<section data-transition="convex">
<h2>CBRAIN portal</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>
</section>
<!--CBRAIN TOOLS-->
<section>
<section>
<h2>CBRAIN - Tools</h2>
<p align="left"><font color="yellow"> Conversion tools:</font></p>
<p align="left">MINC ↔ NIfTI, DICOM → MINC, DICOM → NIfTI, Analyze → HRRT, ASPIRO → MINC, DICOM → HRRT, MINC1 ↔ MINC2</p>
<p align="left"align="left"><font color="yellow">Image Processing tools:</font>
<ul>
<li> Civet, CivetCombiner & CivetQC</li>
<li> FSL: bedpostx, bet, fast, feat, first flirt, melodic, probtrackx</li>
<li> FreeSurfer: recon-all, and recon-all longitudinal</li>
<li> NIAK</li>
<li> Several other project specific tools</li>
</ul>
</section>
<!-- CIVET: Corticometric Iterative Vertex-based Estimations of Topology -->
<section>
<table class="reveal">
<h2>CIVET</h2>
<tr>
<td width="50%" style="vertical-align: middle">
<p><small>The CIVET project was initiated in order to create an automated, easy-to-use human brain-imaging pipeline that makes use of state-of-the-art software tools developed by researchers at the BIC for the fully-automated processing and analysis of large MR data sets, including the extraction and analysis of cortical surfaces from MR images, as well as many other volumetric and corticometric functions.</small></p>
<a href="http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET" target="_blank"><img src="images/CIVET.png"></a>
</td>
<td width="50%" style="vertical-align: top">
<p class="fragment roll-in"><font color="f27c30">Fully automated anatomical pipeline</font></p>
<p class="fragment roll-in"><font color="f27c30">Parallel processing</p>
<p class="fragment roll-in"><font color="f27c30">Can handle large datasets</p>
<p class="fragment roll-in"><font color="f27c30">Includes QC mechanisms</p>
<p class="fragment roll-in"><font color="f27c30">>10 yrs active development</p>
<p class="fragment roll-in"><font color="f27c30">Publication in process</p>
</td>
</tr></table>
</section>
<!-- CIVET (and NIAK?) -->
<section>
<table class="reveal">
<h2>CIVET - Processing steps</h2>
<tr>
<td>
<img src="images/CIVET_processing_steps.png">
</td>
</tr></table>
</section>
<section>
<table class="reveal">
<h2>CIVET - Pipeline schema</h2>
<tr>
<td>
<img src="images/CIVET_steps.png">
</td>
<td style="vertical-align: top">
<img src="images/CIVET_surface.png" width="50%">
<img src="images/CIVET_segmentation.png" width="50%">
</td>
</tr></table>
</section>
<section>
<h2>NIAK</h2>
<a href="http://niak.simexp-lab.org/" target="_blank"><p><small>http://niak.simexp-lab.org/</small></p></a>
<img src="images/NIAK.jpg" width="70%">
</section>
</section>
<!-- FUNCTIONALTIY -->
<section>
<section>
<h2>CBRAIN - Functionality</h2>
<p class="fragment roll-in">Non-expert users can easily leverage Compute Canada</p>
<p class="fragment roll-in">Anyone can request an account (best effort support):<br> <a href="mailto:cbrain-support.mni@mcgill.ca">cbrain-support.mni@mcgill.ca</a> </p>
<p class="fragment roll-in">CBRAIN code is now public: <a href="https://github.com/aces/cbrain" target="blank">https://github.com/aces/cbrain</a> </p>
<p class="fragment roll-in">Includes several structural and functional MRI tools</p>
<p class="fragment roll-in">Continued integration of new tools as per community needs</p>
</section>
</section>
<!-- MINC -->
<section>
<section>
<table class="reveal">
<h2>MINC</h2>
<tr>
<td width="60%" style="vertical-align: middle">
<img src="images/MINC.png">
</td>
<td width="40%" style="vertical-align: middle">
<p><small>The MINC file format and toolbox was originally conceived, written and released by Peter Neelin in 1992.</small></p>
</td>
</tr></table>
</section>
<section>
<h2>Install MINC - BIC systems</h2>
<p class="fragment roll-in">By default binaries are available at <font color="green"> /usr/local/mni </font></p>
<p class="fragment roll-in">Better to use <font color="green"> /usr/local/bic</font></p>
<p class="fragment roll-in">A much more up-to-date version is installed in <font color="green"> /ipl/quarantine/std/x86_64/1.0 </font></p>
<p class="fragment roll-in">To execute: <font color="green"> source /ipl/quarantine/std/x86_64/1.0/init.csh</font></p>
</section>
<section>
<h2>Install MINC - Personal computers</h2>
<p class="fragment roll-in">For personal computers (incl. Macs): <a href ="https://www.mcgill.ca/bic/resources/minc/minctoolkit">https://www.mcgill.ca/bic/resources/minc/minctoolkit</a> </p>
<p class="fragment roll-in">Two versions are mentioned: 1.0 and 1.9.2: install 1.0 version, which includes all the standard MINC tools with support for MINC2.</p>
<p class="fragment roll-in">Main difference: ITK-based software is also included. </p>
<!--
<p class="fragment roll-in">Version 1.0 uses ITK 3.20 and contains mincANTS + some of Vlad's tools that use ITK 1.9.xx contains ITK 4.7 and includes ANTS, Elastix and ABC - but most people don’t need that. </p>
-->
</section>
<section>
<h2>MINC resources</h2>
<ul><small>
<li>minc-users mailing list: <br> <a href="http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users">http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users</a></li> <br>
<li>Current documention on wikibooks: <br> <a href="http://en.wikibooks.org/wiki/MINC">http://en.wikibooks.org/wiki/MINC</a></li> <br>
<li>Current combined release: <br><a href="http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit">http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit</a></li> <br>
<li>Github (for bug report and source code) <br><a href="https://github.com/BIC-MNI/minc-toolkit/">https://github.com/BIC-MNI/minc-toolkit/</a></li> <br>
</small></ul>
</section>
</section>
<section>
<h2> CBRAIN GITHUB </h2>
<p><small><a href="https://github.com/aces/cbrain" target="_blank">https://github.com/aces/cbrain</a><br>
NITRC: <a href="www.nitrc.org/projects/cbrain" target="_blank">www.nitrc.org/projects/cbrain</a></small></p>
</section>
<!-- Acknowledgemnts -->
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
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<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>
</section>
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