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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>MNI Ecosytem - McGill Centre for Integrative Neuroscience</title>
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<section data-background="images/IBIS_image.png">
<h1 style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;">Ludmer Centre for Neuroinformatics and Mental Health</h1>
<h4 style="padding-bottom:0px; margin-bottom:0px;text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;" align="center">McGill Centre for Integrative Neuroscience</h4>
<!--ENTER DATE OF PRESENTATION HERE-->
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><small>Samir Das<br>Director of Technology</small></p>
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><small><b>Montreal Neurological Institute</b></small></p>
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<a href="http://www.mcgill.ca/neuro/" target="_blank"><img src="images/Neuro.png" style="border: 0"></a>
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<a href="http://ludmercentre.ca/" target="_blank"><img src="images/ludmer-new-white.png" style="border: 0"></a>
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<!-- MNI ecosystem menu/summary-->
<section>
<section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
</section>
<!-- MNI PAPER -->
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<a href="https://www.researchgate.net/publication/281780543_The_MNI_data-sharing_and_processing_ecosystem" target="_blank"><img src="images/MNI_ecosystem_paper.png" width="90%"></a>
</section>
</section>
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<a href="LORIS_indepth.html#/2" target="_blank"><h2>WHAT IS LORIS?</h2></a>
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<a href="http://loris.ca/" target="_blank"><img src="images/loris-new-white.png"></a>
<p><small> “..is a modular and <font color="f27c30">extensible</font> web-based data and project management software that integrates all aspects of a <font color="f27c30">multi-center</font> neuroimaging research study. It is an <font color="f27c30">OPEN SOURCE</font> framework and database suitable for managing <font color="f27c30">large datasets</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>
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<section>
<h2>Extensible and modular design</h2>
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<img src="images/BrainBrowser_VolumeViewer.png">
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<img src="images/Imaging_scans.png" width="57%">
</section>
<section data-background="images/LORIS_global_2.jpg">
<h1 style="margin: 275px 0px 0px 0px;"><font color ="0d4983">LORIS Globally</font></h1>
</section>
</section>
<!--CBRAIN-->
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<a href="CBRAIN_indepth.html#/2" target="_blank"><h2>WHAT IS CBRAIN?</h2></a>
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<a href="https://mcin-cnim.ca/technology/cbrain/" target="_blank"><img align="center" src="images/cbrain-blue.png" style="border:0; border-radius:30px;" width="90%"></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>
</td>
<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>
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</table>
</section>
<!-- What does CBRAIN do? -->
<section data-background="images/distributed_execution_2.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="65%">
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<h2><font color="12a3d8">LORIS-CBRAIN INTEGRATION</font></h2>
<img src="images/Data_flow.jpg">
</section>
<section data-background="images/NIAK.jpg">
<h2 style="margin: -380px 0px 200px 0px "><font color="222222">NIAK</font></h2>
<a href="http://niak.simexp-lab.org/" target="_blank"><p style="margin:135px 0px 0px 0px;">http://niak.simexp-lab.org/</p></a>
</section>
</section>
<!--BrainBrowser-->
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<a href = "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>
<img src="images/Brain_browser_sample.png">
</section>
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<!-- BIG BRAIN -->
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<a href="Big_brain.html#/2" target="_blank"><h2><font color="2bfcf8">BigBrain</h2></font></a>
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<p align="center"><small>The <font color="2bfcf8">BigBrain</font> is the digitized reconstruction of <font color="f27c30">7404 hi-res</font> coronal histological sections (20 microns isotropic).</small></p>
<p align="center"><small>It is the brain of a <font color="2bfcf8">65 year-old man</font> with <font color="f27c30">no neurological or psychiatric diseases</font> in clinical records at time of death.</small></p>
<div align="center"><img src="images/BigBrain.png" width="73%" style="border:0;"></div>
</td>
<td width="50%" style="vertical-align: middle">
<a href="http://science.sciencemag.org/content/340/6139/1472" target="_blank"><img src="images/BigBrain_paper.png"></a>
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</section>
<section data-background-video="images/Bigbrain_low.mp4" data-background-color="#000000">
<p class="fragment current-visible"><font size="9" color="blue">BigBrain - high resolution reference brain</font></p>
<p class="fragment current-visible"><font size="9" color="blue">Multimodal integration into an anatomically realistic standard space</font></p>
<p class="fragment current-visible"><font size="9" color="blue">Years of development</font></p>
<p class="fragment current-visible"><font size="9" color="blue">20 micron resolution</font></p>
<p class="fragment current-visible"><font size="9" color="blue">7404 histological slices</font></p>
<p class="fragment current-visible"><font size="9" color="blue">1 Terabyte dataset</font></p>
<p class="fragment current-visible"><font size="9" color="blue"><a href="https://bigbrain.humanbrainproject.org/#!{'layers':{' grey value: ':{'type':'image'_'source':'precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/8bit'_'transform':[[1_0_0_-70666600]_[0_1_0_-70000000]_[0_0_1_-58777700]_[0_0_0_1]]}_' tissue type: ':{'type':'segmentation'_'source':'precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/classif'_'selectedAlpha':0_'segments':['0'_'100']_'transform':[[1_0_0_-70666600]_[0_1_0_-72910000]_[0_0_1_-58777700]_[0_0_0_1]]}}_'navigation':{'pose':{'position':{'voxelSize':[21166.666015625_20000_21166.666015625]_'voxelCoordinates':[-3338.57958984375_856.3231811523438_-853.1627807617188]}}_'zoomFactor':1400706.647149517}_'perspectiveOrientation':[0.3140767216682434_-0.7418519854545593_0.4988985061645508_-0.3195493221282959]_'perspectiveZoom':1922235.5293810747}" target="_blank"><font color="f27c30"><small>Click to launch the Neuroglancer Viewer!</small></font></a></font></p>
</section>
</section>
<!-- STUDIES -->
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<a href="https://pediatricmri.nih.gov/nihpd/info/publications.html" target="_blank"><img src="images/NIHPD_logo.jpg"></a>
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<a href="http://www.sciencedirect.com/science/article/pii/S105381190500710X?via%3Dihub" target="_blank"><img src="images/NIHPD_paper.png"></a>
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<img src="images/MRI_images_several.jpg">
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<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>
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<a href="http://www.ibis-network.org/" target="_blank"><img src="images/IBIS.png"></a>
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<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>
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<img src="images/IBIS_image.png">
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<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>
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</section>
<!--CCNA-->
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<img src="images/ESM.png">
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<img src="images/Alzheimer_cost.png">
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<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>
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<img width="85%" src="images/Nature_open_science.png">
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</section>
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<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>
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