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<!DOCTYPE html>
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<head>
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<title>BrainHack School</title>
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<div class="col-sm-8 col-sm-offset-2" style="margin-top: 20px">
<p class="inner-p">
Les listes suivantes présentent certains thèmes que les participants de l'école Brainhack pourront choisir d'approfondir. Le contenu exact du cours sera défini par le matériel requis par chaque projet.
</p>
<div id="accordion" role="tablist" aria-multiselectable="true" class="panel-group">
<div class="panel panel-default">
<div id="headingOne" role="tab" class="panel-heading">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseOne" aria-expanded="true" aria-controls="collapseOne" class="collapsed">Données ouvertes</a>
</h4>
</div>
<div id="collapseOne" role="tabpanel" aria-labelledby="headingOne" class="panel-collapse collapse" aria-expanded="true" style="height: 0px;">
<div class="panel-body">
Ressources disponibles:
<ul>
<li> <a href="https://www.mcgill.ca/bic/resources/omega"> Omega</a>: the open magneto-encephalography archive. </li>
<li> <a href="http://fcon_1000.projects.nitrc.org/"> INDI</a>: the international data sharing initiative. </li>
<li> <a href="http://fcon_1000.projects.nitrc.org/indi/CoRR/html/concept.html"> CORR</a>: Consortium for Reliability and Reproducibility. </li>
<li> <a href="http://fcon_1000.projects.nitrc.org/indi/abide/"> ABIDE</a>: Autism Brain Imaging Data Exchange. </li>
<li> <a href="http://fcon_1000.projects.nitrc.org/indi/adhd200/"> ADHD200</a>: Imaging data sharing in Attention Deficit and Hyperactivity Disorder. </li>
<li> <a href="http://fcon_1000.projects.nitrc.org/indi/enhanced/"> NKI enhanced</a>: community-based, lifespan imaging sample. </li>
<li> <a href="https://openneuro.org"> OpenNeuro</a>: various open imaging datasets. </li>
<li> <a href="https://neurovault.org/"> Neurovault</a>: open brain maps (mostly activation maps). </li>
<li> <a href="http://neurosynth.org"> Neurosynth</a>: published activation coordinates and meta-analysis. </li>
</ul>
Outils pour le partage de données:
<ul>
<li> <a href="https://brainder.org/2012/09/23/the-nifti-file-format/"> NIFTI format</a> for brain images </li>
<li> <a href="https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference"> MINC format</a> for brain images </li>
<li> <a href="http://bids.neuroimaging.io/"> BIDS</a>: Brain Imaging Data Structure </li>
<li> <a href="https://figshare.com/"> Figshare</a>: generic platform for data sharing</li>
<li> <a href="https://zenodo.org/"> zenodo</a>: generic platform for data sharing</li>
<li> Databases and REST API, e.g. <a href="https://docs.figshare.com/"> Figshare's API</a></li>
<li> The <a href="http://loris.ca/"> LORIS</a> database.</li>
</ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div id="headingTwo" role="tab" class="panel-heading">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseTwo" aria-expanded="false" aria-controls="collapseTwo" class="">Code ouvert</a>
</h4>
</div>
<div id="collapseTwo" role="tabpanel" aria-labelledby="headingTwo" class="panel-collapse collapse" aria-expanded="false">
<div class="panel-body">
Développement logiciel:
<ul>
<li> <a href="http://github.com"> Github</a>: version control and social coding. </li>
<li> <a href="https://docsify.js.org/#/"> Docsify</a>: Building software documentation. </li>
<li> <a href="http://nose.readthedocs.io/en/latest/testing.html"> Nose</a>: Building automated tests for software. </li>
<li> <a href="https://circleci.com"> Circle CI</a>: Continuous integration testing</li>
</ul>
Partage de code:
<ul>
<li> <a href="https://singularity.lbl.gov/"> Singularity</a>: containers. </li>
<li> <a href="https://www.docker.com/"> Docker</a> containers. </li>
<li> <a href="http://jupyter.org/"> Jupyter</a> notebooks. </li>
<li> <a href="https://mybinder.org/"> Binder</a> notebooks. </li>
</ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div id="headingThree" role="tab" class="panel-heading">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseThree" aria-expanded="false" aria-controls="collapseThree" class="collapsed">Calcul à haute performance</a>
</h4>
</div>
<div id="collapseThree" role="tabpanel" aria-labelledby="headingThree" class="panel-collapse collapse" aria-expanded="false">
<div class="panel-body">
<ul>
<li> <a href="https://www.computecanada.ca/"> Compute Canada resources</a>. </li>
<li> Industrial cloud computing solutions (<a href="https://aws.amazon.com/"> AWS</a>, <a href="https://azure.microsoft.com/en-ca/"> Azure</a> ). </li>
<li> <a href="https://fcp-indi.github.io/"> CPAC</a>: the configurable pipeline for the analysis of connectomes.</li>
<li> <a href="http://nipype.readthedocs.io/en/latest/"> Nipype</a>: Building neuroimaging pipelines in python. </li>
<li> <a href="https://mcin-cnim.ca/technology/cbrain/"> CBRAIN</a>: neuroimaging science gateway. </li>
<li> <a href="https://openneuro.org/"> Open Neuro</a>: neuroimaging science gateway. </li>
<li> <a href="https://bids-apps.neuroimaging.io/"> BIDS apps</a>: collection of neuroimaging pipelines. </li>
<li> <a href="https://boutiques.github.io/"> Boutiques</a>: automated tool validation and deployment</li>
</ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div id="headingFour" role="tab" class="panel-heading">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseFour" aria-expanded="false" aria-controls="collapseFour" class="collapsed">Visualisation de données</a>
</h4>
</div>
<div id="collapseFour" role="tabpanel" aria-labelledby="headingFour" class="panel-collapse collapse" aria-expanded="false">
<div class="panel-body">
<ul>
<li> <a href="https://plot.ly/"> Plotly</a>: interactive web-based figures. </li>
<li> <a href="http://visbrain.org/"> Visbrain</a>: brain visualization in python. </li>
<li> <a href="https://nilearn.github.io/auto_examples/index.html#visualization-of-brain-images"> Nilearn</a>: Brain visualization in python.</li>
<li> <a href="http://jupyter.org/widgets"> Interactive visualization for jupyter notebooks. </li>
<li> <a href="https://altair-viz.github.io/"> Altair </a> Interactive visualization in python. </li>
</ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div id="headingFive" role="tab" class="panel-heading">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseFive" aria-expanded="false" aria-controls="collapseFive" class="collapsed">Apprentissage machine</a>
</h4>
</div>
<div id="collapseFive" role="tabpanel" aria-labelledby="headingFive" class="panel-collapse collapse" aria-expanded="false">
<div class="panel-body">
<ul>
<li> <a href="https://pandas.pydata.org/"> Pandas</a>: data analysis in python.</li>
<li> Regression, cross validation and generalization error.</li>
<li> Support vector machine, naive Bayes, random forest.</li>
<li> Cluster analysis, component analysis. </li>
<li> Deep neural networks, convolutional networks and gradient descent. </li>
<li> <a href="http://scikit-learn.org"> Scikit-learn</a>: machine learning with python. </li>
<li> <a href="http://pytorch.org/"> Pytorch</a>: deep learing library. </li>
</ul>
</div>
</div>
</div>
<div class="panel panel-default">
<div id="headingSix" role="tab" class="panel-heading">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseSix" aria-expanded="false" aria-controls="collapseFive" class="collapsed">Neuroimagerie</a>
</h4>
</div>
<div id="collapseSix" role="tabpanel" aria-labelledby="headingSix" class="panel-collapse collapse" aria-expanded="false">
<div class="panel-body">
<ul>
<li> <a href="https://www.martinos.org/mne/">MNE</a>: MEG and EEG analysis and visualization in python.</li>
<li> <a href="https://github.com/neuropoly/qMRLab">qMRLab</a>: open-source Matlab software for quantitative MR image analysis.</li>
<li> <a href="https://nilearn.github.io/"> nilearn </a> machine learning for neuroimaging, in python.</li>
<li> fMRI preprocessing and feature extraction. </li>
<li> M/EEG preprocessing and feature extraction. </li>
<li> structural MRI preprocessing and feature extraction. </li>
</ul>
</div>
</div>
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