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<!DOCTYPE HTML>
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Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
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<html>
<head>
<title>IMPAC - Imaging-psychiatry challenge: predicting autism</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<body>
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<!-- <span class="icon major fa-cloud"></span> -->
<img src="images/brain.png">
<h1><strong>IMPAC</strong></h1>
<h1><strong>IMaging-PsychiAtry Challenge: predicting
autism</strong></h1>
<h2>A data challenge on Autism Spectrum Disorder detection</h2>
<h3>Deadline: July 1, 2018 - 8 pm (UTC)</h3>
<div id="clockdiv">
<div>
<span class="days"></span>
<div class="smalltext">Days</div>
</div>
<div>
<span class="hours"></span>
<div class="smalltext">Hours</div>
</div>
<div>
<span class="minutes"></span>
<div class="smalltext">Minutes</div>
</div>
<div>
<span class="seconds"></span>
<div class="smalltext">Seconds</div>
</div>
</div>
<ul class="actions">
<li><a href="#one" class="button scrolly">Discover</a></li>
</ul>
</div>
</section>
<!-- One -->
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<div class="container">
<div class="row 150%">
<div class="12u 12u$(medium)">
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<h2><span class="fa fa-database"></span> A big data
challenge</h2>
</header></center>
<header class="major">
<h3><span class="fa fa-chart-pie"></span> Brain images from
more than 2000 individuals</h3>
</header>
<center>
<div class="row 150%">
<div class="4u 12u$(medium)">
<h3>Patient vs Control distribution</h3>
<img src="images/01_target.png" width="100%">
</div>
<div class="4u 12u$(medium)">
<h3>Gender distribution</h3>
<img src="images/04_sex.png" width="100%">
</div>
<div class="4u 12u$(medium)">
<h3>Age distribution</h3>
<img src="images/05_age.png" width="100%">
</div>
</div>
</center>
<header class="major">
<h3><span class="fa fa-images"></span> Multimodal imaging data</h3>
</header>
<div class="row 150%">
<div class="1u 12u$(medium)"><br /></div>
<div class="5u 12u$(medium)">
<center><h3>Structural MRI</h3></center>
<ul>
<li>Preprocessed with FreeSurfer and FSL</li>
<li>Gray matter volume, area, and thickness
<li>Average for each Desikan cortical parcel.</li>
</ul>
</div>
<div class="5u 12u$(medium)">
<center><h3>Functional MRI</h3></center>
<ul>
<li>Resting state fMRI</li>
<li>Time series extracted on different atlases</li>
</ul>
</div>
<div class="1u 12u$(medium)"><br /></div>
</div>
<div class="row 150%">
<header class="major">
<h3><span class="fa fa-code" id="starting_kit"></span>
Coding framework, for competition and collaboration</h3>
</header>
<p>The challenge will be carried out on
the <a href="https://ramp.studio"><b>RAMP platform</b></a>. It
enables competition and collaboration on data-science problems,
using the Python language. To start "hacking", a starting kit
is available. It provides a simple working example which can be
expanded to more advanced solutions.</p>
<div class="5u 5u$(medium)"><br /></div>
<ul class="actions">
<li><a
href="http://nbviewer.jupyter.org/github/ramp-kits/autism/blob/master/autism_starting_kit.ipynb"
class="button
special fit">Starting kit</a></li>
</ul>
<div class="5u 5u$(medium)"><br /></div>
</div>
</div>
</div>
</div>
</section>
<!-- Two -->
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<li><span class="icon style1 major fa-question-circle-o"></span></li>
</ul>
</div>
<div class="8u 8u">
<header class="major">
<h2>What is this challenge?</h2>
</header>
<p>
Autism spectrum disorder (ASD) is a severe psychiatric
disorder that affects 1 in 166 children.
</p>
<p>
There is evidence that ASD is reflected in
individuals brain networks and anatomy. Yet, it remains
unclear how systematic these effects are, and how large is
their predictive remain unclear. The large cohort
assembled here can bring some anwsers. Predicting
autism from brain imaging will provide biomarkers and
shed some light on the mechanisms of the pathology.
</p>
</div>
</div>
</div>
<div class="container">
<div class="row 150%">
<div class="4u 4u">
<ul class="major-icons">
<li><span class="icon style2 major fa-sign-in"></span></li>
</ul>
</div>
<div class="8u 8u">
<header class="major">
<h2>Joining the competition</h2>
</header>
<p>
The goal of the competition is to predict the diagnostic
status from brain imaging data in the hidden test set. The
data of the test set are on
a server, hidden from participants. Prediction is done by
submitting Python code that will be first trained by the
server on training images, and then applied to predict on the
hidden test set.
</p>
</div>
</div>
</div>
<div class="container">
<div class="row 150%">
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<ul class="major-icons">
<li><span class="icon style3 major fa-trophy"></span></li>
</ul>
</div>
<div class="8u 8u">
<header class="major">
<h2>Prizes</h2>
</header>
<p>
The best performers will be awarded prizes at the end of
the competitive period,
based on the metrics used during the challenge: 1<sup>st</sup> - 3000 €, 2<sup>nd</sup>
- 2000 €, 3<sup>rd</sup> - 1000 €, from 4<sup>th</sup>
to 10<sup>th</sup>- 500 €.
</p>
</div>
</div>
</div>
<div class="container">
<div class="row 150%">
<div class="4u 4u">
<ul class="major-icons">
<li><span class="icon style4 major fa-calendar"></span></li>
</ul>
</div>
<div class="8u 8u">
<header class="major">
<h2>The timeline</h2>
</header>
<p>
This challenge is made of 2 phases:
<ol>
<li>a <strong>competitive phase</strong> up to
July 1 in which participants can submit their solutions to
the <a href="https://ramp.studio/">RAMP</a> platform. A Q&A
session regarding the challenge and technical platform is
organized May 14;</li>
<li> a <strong>collaborative phase</strong> from July 1 to July
7. This last day will coincide with the awards ceremony.
</li>
</ol>
</p>
</div>
</div>
</div>
<div class="container">
<div class="row 150%">
<div class="4u 4u">
<ul class="major-icons">
<li><span class="icon style5 major fa-map-marker"></span></li>
</ul>
</div>
<div class="8u 8u">
<header class="major">
<h2>2 events in Paris</h2>
</header>
<p>
Anyone can participate remotely. In addition, two events will
be organized as follows:
<ul>
<li>May 14, 2018: a Q&A with the team to help get
started, <a href="https://goo.gl/maps/NAWuNjBykap">La
Paillasse, 226 rue Saint-Denis, 75002 Paris</a></li>
<li>July 6 & 7,
2018: collaboration after the competition,
<a href="https://goo.gl/maps/CGLn34ZDswT2">Institut
Pasteur, 25-28 Rue du Dr Roux, 75015 Paris</a></li>
</ul>
<!-- <div class="row 150%"> -->
<!-- <ul class="actions"> -->
<!-- <li><a -->
<!-- href="https://indico.lal.in2p3.fr/event/4845/" -->
<!-- class="button -->
<!-- special fit">Register for La Paillasse event</a></li> -->
<!-- </ul> -->
<!-- </div> -->
</p>
<!-- <h3>How to join the events?</h3>
<p>
You need to register for the event before May 31, 2018. Catering
will be provided.
</p>
<ul class="actions">
<li><a href="https://indico.lal.in2p3.fr/event/4845/"
class="button">Register now</a></li>
</ul> -->
</div>
</div>
</div>
</section>
<!-- Three -->
<section id="three" class="main style1">
<div class="container">
<div class="row 150%">
<div class="12u 12u$(medium)">
<center><header class="major">
<h2><span class="fa fa-search"></span> More about the data</h2>
</header></center>
</div>
</div>
<div class="row 150%">
<div class="6u 12u$(medium)">
<center><header class="major">
<h3>Structural MRI (sMRI)</h3>
</header></center>
<p>
For each subject, a set of structural features have been
extracted and stored in a CSV file. Each row corresponds to a
subject and each column to a specific features. The features
extracted are:
<ul>
<li>Normalized brain volume computed using subcortical
segmentation of FreeSurfer;</li>
<li>Cortical thickness and area for right and left hemisphere
of FreeSurfer.</li>
</ul>
</p>
</div>
<div class="6u 12u$(medium)">
<center><header class="major">
<h3>Functional MRI (fMRI)</h3>
</header></center>
<p>
Each subject also comes with fMRI signals extracted on
different brain parcellations and atlases, and a set of
confound signals. The brain atlases and
parcellations are:
<ul>
<li>BASC parcellations with 64, 122, and 197 regions
(<a href="http://dx.doi.org/10.1016/j.neuroimage.2010.02.082">Bellec
2010</a>);</li>
<li>Ncuts parcellations
(<a href="https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.21333">Craddock
2012</a>);</li>
<li>Harvard-Oxford anatomical parcellations;</li>
<li>MSDL functional atlas
(<a href="http://dx.doi.org/10.1007/978-3-642-22092-0_46">Varoquaux
2011</a>);</li>
<li>Power atlas
(<a href="http://www.cell.com/neuron/fulltext/S0896-6273(11)00792-6">Power
2011</a>).</li>
</ul>
The <a href="http://nilearn.github.io/modules/reference.html#module-nilearn.datasets">Nilearn
documentation</a> gives details on the parcellations,
and <a href="https://github.com/ramp-kits/autism/blob/master/preprocessing/extract_time_series.py">how
they were extracted</a>.
</p>
<p>
The time series for each subject are stored in a CSV file. Each
row represent a scan while each column a region defined by the
brain parcellation or atlas used.
</p>
</div>
</div>
<div class="row 150%">
<div class="12u 12u$(medium)">
<center><header class="major">
<h3>Multimodal: predicting from sMRI and fMRI data</h3>
</header></center>
<p>
The data are openly downloadable and a Jupyter notebook
provides
a <strong><a href="#starting_kit">starting kit</a></strong>.
It explain: (i) how to read data, (ii) how design, train, and
test a model, (iii) how to submit it on the competition platform.
</p>
<p>
Refer to
the <a href="http://nbviewer.jupyter.org/github/ramp-kits/autism/blob/master/autism_starting_kit.ipynb">starting
kit</a> for more information.
</p>
</div>
<div class="5u 5u$(medium)"><br /></div>
<ul class="actions">
<li><a
href="https://github.com/ramp-kits/autism/issues"
class="button
special fit">Questions</a></li>
</ul>
<div class="5u 5u$(medium)"><br /></div>
</div>
</div>
</section>
<!-- Four -->
<section id="four" class="main style2 special trombinoscope">
<div class="container">
<header class="major">
<h2><span class="fa fa-hands-helping"></span>Organizers</h2>
</header>
<header class="major">
<h3>Institutions</h3>
</header>
<div class="row 150%">
<!-- <div class="3u 12u$(medium)"> -->
<!-- <img src="images/brainhack_logo.png" width=100%"> -->
<!-- <p> -->
<!-- The Brainhack Networks is an independent event sponsored by the -->
<!-- organizing committee of NetSci 2018. The hackathon will cover a -->
<!-- topics related to network science tools for -->
<!-- neuroscience research. -->
<!-- </p> -->
<!-- <ul class="actions"> -->
<!-- <li><a href="http://brainhack-networks.com/" class="button">More</a></li> -->
<!-- </ul> -->
<!-- </div> -->
<div class="3u 12u$(medium)">
<img src="images/institut_pasteur_logo.svg" width="70%">
<p>
The group of Neuroanatomy of the Unit of Human Genetics and
Cognitive Functions is interested in the development and
evolution of brain anatomy. We are particularly interested in
Autism Spectrum Disorders.
</p>
<ul class="actions">
<li><a href="https://research.pasteur.fr/en/team/group-roberto-toro/" class="button">More</a></li>
</ul>
</div>
<div class="3u 12u$(medium)">
<img src="images/robert_debre_logo.png" width="90%">
<p>
The Robert Debre Hospital investigates different fields such as
genetic, brain imaging, neurocognitive science to identify new
biomarkers as well as cell models for new therapeutical targets.
</p>
<ul class="actions">
<li><a href="http://robertdebre.aphp.fr/" class="button">More</a></li>
</ul>
</div>
<div class="3u 12u$(medium)">
<img src="images/cds_logo.png" width="120%" style="margin:20px 0px">
<p>
The Paris-Saclay CDS aims at developing methods and tools so as
to be capable of analyzing large amounts of data and extracting
useful information from them for multidisciplinary sciences.
</p>
<ul class="actions">
<li><a href="https://www.datascience-paris-saclay.fr/" class="button">More</a></li>
</ul>
</div>
<!-- <div class="3u$ 12u$(medium)"> -->
<!-- <img src="images/ramp_logo.png" width=100%"> -->
<!-- <p> -->
<!-- RAMPs are organized by the Paris Saclay Center for Data Science: -->
<!-- A multi-disciplinary initiative to define, structure, and manage -->
<!-- the data science ecosystem at the University Paris-Saclay. -->
<!-- </p> -->
<!-- <ul class="actions"> -->
<!-- <li><a href="https://ramp.studio/" class="button">More</a></li> -->
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<!-- </div> -->
<div class="3u 12u$(medium)">
<img src="images/iesf_logo.png" width="80%">
<p>
Ingenieurs et Scientifiques de France (IESF) is the unique
representative of the engineers and scientists social corps. The
IESF is a major actor of the scientific, technological, and
economic debates.
</p>
<ul class="actions">
<li><a href="https://www.iesf.fr/" class="button">More</a></li>
</ul>
</div>
</div>
<div class="row 150%">
<div class="12u 12u$(medium)">
<header class="major">
<h3>People</h3>
</header>
</div>
</div>
<div class="row 150%">
<article class="4u 12u$(xsmall) 6u(medium) special" id="toro">
<a href="#toro" class="image circled crop shadowed">
<img src="images/experts/toro.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://research.pasteur.fr/en/team/group-roberto-toro/">Roberto Toro</a></h3>
</header>
<p>
Institut Pasteur, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="traut">
<a href="#traut" class="image circled crop shadowed">
<img src="images/experts/traut.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://research.pasteur.fr/en/member/nicolas-traut/">Nicolas Traut</a></h3>
</header>
<p>
Institut Pasteur, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="beggiato">
<a href="#beggiato" class="image circled crop shadowed">
<img src="images/experts/beggiato.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://research.pasteur.fr/fr/emember/anita-beggiato/">Anita Beggiato</a></h3>
</header>
<p>
Institut Pasteur, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="heuer">
<a href="#heuer" class="image circled crop shadowed">
<img src="images/experts/heuer.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://www.cbs.mpg.de/person/heuer/373360">Katja Heuer</a></h3>
</header>
<p>
Max Planck Institute, Germany
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="varoquaux">
<a href="#varoquaux" class="image circled crop shadowed">
<img src="images/experts/varoquaux.jpg" alt="portrait" />
</a>
<header>
<h3><a href="http://gael-varoquaux.info/">Gael Varoquaux</a></h3>
</header>
<p>
Inria Parietal, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="gramfort">
<a href="#gramfort" class="image circled crop shadowed">
<img src="images/experts/gramfort.jpg" alt="portrait" />
</a>
<header>
<h3><a href="http://alexandre.gramfort.net/">Alexandre Gramfort</a></h3>
</header>
<p>
Inria Parietal, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="kegl">
<a href="#kegl" class="image circled crop shadowed">
<img src="images/experts/kegl.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://users.lal.in2p3.fr/kegl/">Balazs Kegl</a></h3>
</header>
<p>
LAL, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="lemaitre">
<a href="#lemaitre" class="image circled crop shadowed">
<img src="images/experts/lemaitre.jpg" alt="portrait" />
</a>
<header>
<h3><a href="http://glemaitre.github.io/">Guillaume Lemaitre</a></h3>
</header>
<p>
Paris-Saclay Center for Data Science, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="vandenbossche">
<a href="#vandenbossche" class="image circled crop shadowed">
<img src="images/experts/vandenbossche.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://www.linkedin.com/in/jorisvandenbossche/">Joris Van den Bossche</a></h3>
</header>
<p>
Paris-Saclay Center for Data Science, France
</p>
</article>
<article class="4u 12u(xsmall) 6u(medium) special" id="boucaud">
<a href="#boucaud" class="image circled crop shadowed">
<img src="images/experts/boucaud.jpg" alt="portrait" />
</a>
<header>
<h3><a href="https://www.linkedin.com/in/aboucaud/">Alexandre Boucaut</a></h3>
</header>
<p>
Paris-Saclay Center for Data Science, France
</p>
</article>
</div>
</div>
</section>
<!-- Five -->
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<div class="container">
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<div class="12u 12u$(medium)">
<center><header class="major">
<h2><span class="fa fa-question-circle"></span> Frequently Asked
Questions</h2>
</header></center>
</div>
</div>
<div class="row 150%">
<div class="12u 12u">
<p>We report the most frequent questions related to the IMPAC
challenge. You can visit
the <a href="https://github.com/ramp-kits/autism/issues">GitHub issue
tracker</a> for additional information.</p>
<header class="major">
<h4>How do I register for the IMPAC challenge?</h4>
</header>
<p>You need to register on the <a href="https://ramp.studio">RAMP
platform</a> and sign up for
the <a href="https://ramp.studio/events/autism">IMPAC
challenge</a>.
</p>
<header class="major">
<h4>Can we access the raw data or additional features?</h4>
</header>
<p>Unfortunately, we cannot share the raw imaging data. This is
mostly for privacy and ethical reasons.</p>
</div>
<header class="major">
<h4>Can we use any third-party library?</h4>
</header>
<p>Any open-source library available in <code>conda</code>
or <code>pip</code> can be added to the platform. Please open a
ticket on
the <a href="https://github.com/ramp-kits/autism/issues">GitHub
issue tracker</a>.</p>
</div>
</div>
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<!-- <td>29.99</td> -->
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<!-- <td>19.99</td> -->
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<!-- <td>29.99</td> -->
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<!-- <td>19.99</td> -->
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<!-- <td>29.99</td> -->
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<!-- <tfoot> -->
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<!-- <td colspan="2"></td> -->
<!-- <td>100.00</td> -->
<!-- </tr> -->
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<!-- </table> -->
<!-- </div> -->
<!-- <h5>Alternate</h5> -->
<!-- <div class="table-wrapper"> -->
<!-- <table class="alt"> -->
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<!-- <th>Description</th> -->
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<!-- <tbody> -->
<!-- <tr> -->
<!-- <td>Item One</td> -->
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<!-- <td>29.99</td> -->
<!-- </tr> -->
<!-- <tr> -->
<!-- <td>Item Two</td> -->
<!-- <td>Vis ac commodo adipiscing arcu aliquet.</td> -->
<!-- <td>19.99</td> -->
<!-- </tr> -->
<!-- <tr> -->
<!-- <td>Item Three</td> -->
<!-- <td> Morbi faucibus arcu accumsan lorem.</td> -->
<!-- <td>29.99</td> -->
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<!-- <tr> -->
<!-- <td>Item Four</td> -->
<!-- <td>Vitae integer tempus condimentum.</td> -->
<!-- <td>19.99</td> -->
<!-- </tr> -->
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<!-- <td>Ante turpis integer aliquet porttitor.</td> -->
<!-- <td>29.99</td> -->
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<!-- </tbody> -->
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<!-- <td colspan="2"></td> -->
<!-- <td>100.00</td> -->
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<!-- <h4>Buttons</h4> -->
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