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Human_brain_data.html
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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Open Neuroscience</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">
<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;">Human Brain Data</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">INCF - Brains United Meeting</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>August 2019</small></p>
<p style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><small>Samir Das<br>Associate 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>McGill Centre for Integrative Neuroscience</b><br><b>Montreal Neurological Institute</b></small></p>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align: middle">
<a href="https://mcin-cnim.ca/" target="_blank"><img src="images/MCIN.png" style="border: 0"></a>
</td>
<td width="15%" style="vertical-align: middle">
<a href="http://www.mcgill.ca/neuro/" target="_blank"><img src="images/Neuro.png" style="border: 0"></a>
</td>
<td width="35%" style="vertical-align: middle">
<a href="http://ludmercentre.ca/" target="_blank"><img src="images/ludmer-new-white.png" style="border: 0"></a>
</td>
</tr>
</table>
</section>
<!-- Overarching points -->
<section>
<!-- Multi-resolution/trajectories -->
<section data-transition="convex">
<img src="images/Neuroinformatics_scope.jpg" width="77%">
</section>
<!-- Mapping issues -->
<section data-transition="zoom">
<h2>Mapping Issues</h2>
<table class="reveal" style="margin:-20px 0px -20px 0px;">
<tr>
<td width="49%" style="vertical-align: top">
<img src="images/Mapping_problem.png">
</td>
<td width="51%" style="vertical-align: middle">
<img src="images/Heschl.png">
</td>
</tr>
</table>
</section>
<section data-transition="fade">
<h2>How available is the data?</h2>
<table class="reveal">
<tr>
<td width="33%" style="vertical-align: middle">
<img src="images/Data_Use_agreement.png">
</td>
<td width="33%" style="vertical-align: middle">
<img src="images/Registered_access.png">
</td>
<td width="33%" style="vertical-align: middle">
<img src="images/Open_science.png">
</td>
</tr>
<tr>
<td width="33%" style="vertical-align: middle">
<h4>Data Use Agreements</h4>
</td>
<td width="33%" style="vertical-align: middle">
<h4>Registered Access</h4>
</td>
<td width="33%" style="vertical-align: middle">
<h4>Open Access</h4>
</td>
</tr>
</table>
</section>
<section>
<h2>How raw is the data?</h2>
<img src="images/Rawness.png">
</section>
<!-- Quality -->
<section data-transition="zoom">
<h2>Quality</h2>
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<img src="images/QC.png">
</td>
<td width="51%" style="vertical-align: middle">
<img src="images/volume_viewer_2.png">
<p>Resolution<br></p>
<p>Completeness<br></p>
<p>Artifact-free<br></p>
<p>Well documented<br></p>
<p>Provenance<br></p>
</td>
</tr>
</table>
</section>
<!-- FAIR -->
<section data-transition="fade">
<img src="images/FAIR.png">
</section>
<!-- COBIDAS -->
<section data-transition="zoom">
<img src="images/COBIDAS_Nature_new.png">
</section>
</section>
<!-- Atlases and Templates -->
<section data-transition="convex" id="openscience-destination">
<section>
<h2>Atlases and Templates</h2>
<img src="images/Templates_atlases.png">
</section>
<!-- Talairach -->
<section data-transition="concave">
<img src="images/Talairach.png">
</section>
<!-- MNI atlases -->
<section data-transition="fade">
<img src="images/MNI_atlases.png">
</section>
<!-- Allen Institute -->
<section data-transition="convex">
<img src="images/Allen_institute.png">
</section>
<!-- NIHPD age specific templates -->
<section data-transition="fade">
<img src="images/MRI_images_several.jpg" width="60%">
</section>
<!-- Poldrack Phantom -->
<section data-transition="fade">
<img src="images/Poldrack.png">
</section>
<!-- SIMON data -->
<section data-transition="zoom">
<img src="images/SIMON_data.png">
</section>
<!-- Sombrero -->
<section>
<img src="images/Sombrero.jpg">
</section>
<!-- Phantom -->
<section>
<img src="images/Phantom.png">
</section>
</section>
<!-- Large Scale Datasets -->
<section data-transition="fade">
<section>
<h2>Large Scale Datasets</h2>
</section>
<!-- UK Biobank -->
<section data-transition="fade">
<img src="images/UK_biobank.png">
</section>
<!-- HBHL -->
<section data-transition="fade">
<img src="images/HBHL.png">
</section>
<!-- HCP -->
<section data-transition="zoom">
<img src="images/HCP.png">
</section>
</section>
<!-- More manageable datasets -->
<section data-transition="concave">
<section data-transition="fade">
<h2>More Manageable Datasets</h2>
</section>
<!-- ADNI -->
<section>
<img src="images/ADNI_paper.png">
</section>
<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="concave">
<a href="http://ccna-ccnv.ca/en/" target="_blank"><img src="images/CCNA.png" width="85%"></a>
</section>
<!--ABCD-->
<section data-transition="convex">
<a href="https://abcdstudy.org" target="_blank"><img src="images/ABCD.png" width="85%"></a>
</section>
</section>
<!-- BIG BRAIN -->
<section data-transition="convex">
<section>
<table class="reveal">
<a href="Big_brain.html#/2" target="_blank"><h2><font color="2bfcf8">BigBrain</h2></font></a>
<tr>
<td width="50%" style="vertical-align: middle">
<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>
</td>
</tr>
</table>
</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>
<!-- BigBrain layers -->
<section data-transition="convex">
<img src="images/Bigbrain_layers.png">
</section>
<!-- Deep learning -->
<section data-transition="convex">
<img src="images/Bigbrain_AI.png">
</section>
</section>
<!-- AI -->
<section data-transition="concave">
<section data-transition="convex">
<h2>Deep Learning</h2>
</section>
<section data-transition="convex">
<img src="images/NeuroMod.png">
</section>
<section data-transition="convex">
<img src="images/nilearn.png">
</section>
<section data-transition="convex">
<img src="images/Shithead.png">
</section>
</section>
<!-- Other Datasets -->
<section data-transition="concave">
<section>
<h2>Other Datasets worth mentioning</h2>
</section>
<!-- PreventAD -->
<section data-transition="zoom">
<table class="reveal" style="margin:-20px 0px -20px 0px;">
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<img src="images/Open_PreventAD_list.png">
</td>
<td width="51%" style="vertical-align: middle">
<img src="images/Open_PreventAD_dashboard.png">
</td>
</tr>
</table>
<img src="images//Open_PreventAD_LORIS.png" width="80%">
</section>
<!-- Cuban Brain Mapping -->
<section data-transition="convex">
<a href="" target="_blank"><img src="images/Cuban_brain_mapping.png" width="120%"></a>
</section>
<!-- ABIDE -->
<section data-transition="convex">
<a href="http://preprocessed-connectomes-project.org/abide/" target="_blank"><img src="images/ABIDE_preprocessed.png"></a>
</section>
<!-- iEEG -->
<section data-transition="convex">
<h2>Open iEEG atlas</h2>
<a href="https://mni-open-ieegatlas.research.mcgill.ca" target="_blank"><img src="images/iEEG.png" width="150%"></a>
</section>
<!-- ADHD -->
<section data-transition="zoom">
<table class="reveal" style="margin:-20px 0px -20px 0px;">
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<img src="images/ADHD.png">
</td>
<td width="51%" style="vertical-align: middle">
<img src="images/ADHD_preprocessed.png">
</td>
</tr>
</table>
</section>
</section>
<!-- Where to find data?-->
<section>
<section data-transition="zoom">
<h2>Where to find data?</h2>
</section>
<!-- Open Neuro -->
<section data-transition="convex">
<a href="https://openneuro.org" target="_blank"><img src="images/Open_neuro_2019.png" width="120%"></a>
</section>
<section data-background="images/CONP.png" data-background-size="100%">
</section>
<!-- INDI -->
<section data-transition="convex">
<a href="http://fcon_1000.projects.nitrc.org" target="_blank"><img src="images/INDI.png" width="120%"></a>
</section>
<!-- OpenMorph -->
<section data-transition="convex">
<a href="https://github.com/cMadan/openMorph/blob/master/README.md" target="_blank"><img src="images/OpenMorph.png" width="120%"></a>
</section>
<!-- Open Neuro -->
<section data-transition="convex">
<a href="https://nda.nih.gov" target="_blank"><img src="images/NDAR.png" width="120%"></a>
</section>
<!-- Zenodo/Figshare -->
<section data-transition="slide" data-background-transition="zoom">
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<img src="images/Zenodo.png">
</td>
<td width="51%" style="vertical-align: middle">
<img src="images/Figshare.png">
</td>
</tr>
</table>
</section>
<!-- Google Dataset search -->
<section data-transition="convex">
<a href="https://toolbox.google.com/datasetsearch" target="_blank"><img src="images/Google_data.png" width="120%"></a>
</section>
</section>
</section>
<!--Acknowledgements-->
<section data-transition="zoom">
<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="85%">
</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, JB Poline, Shawn Brown, Louis Collins, Vladimir Fonov, Pierre Rioux, Claude Lepage, Tristan Glatard, Jason Karamchandani, Cecile Madjar, Ted Fon, John Brietner, 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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