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5steps.html
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<!DOCTYPE html>
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This page under construction, beware...
<br>
See this <a href="https://docs.google.com/document/d/1i2DVI1b4fBJuLAjKRcjPE6oV8233POa2hVrwz4ve2Xo/edit">link</a> for a publically-commentable draft of the future page...
<h1 class="main-page-header">5 Steps to More Reproducible Neuroimaging Research</h1>
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<div class="col-md-12">
<p>
Going whole-hog into completely reproducible neuroimaging is hard. But, there are lots of little things you can do today to increase the reproducibility of your current studies.
</p>
<table style="width:100%;background-color:#f6f945;font-size:30px">
<tr>
<td><b>Study Design</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/design">repronim.org/5Steps/design</a></td>
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<!-- <h2 style="background-color:#f6f945">Study Design</h2> -->
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<li>Build data shareability into the consent process - see <a href="http://open-brain-consent.readthedocs.io">Open Brain Consent</a>, for example.
<li>Plan your study with a RoadMap - see, for example, <a href="http://brainverse.repronim.org">BrainVerse</a>.
<li>Pre-register your study - at, for example, <a href="http://osf.io">Open Science Foundation</a>.
</ul>
</p>
<table style="width:100%;background-color:#3ffff5;font-size:30px">
<tr>
<td><b>Data Collection</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/acquisition">repronim.org/5Steps/acquisition</a></td>
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<li>Adopt standards-based data representation from the get go.
<li>Use <a href="http://reproin.repronim.org">ReproIn</a> to automate conversion of your imaging data to <a href="http://bids.neuroimaging.io">BIDS</a>.
<li>Annotate your metadata (all experimental details) as you collect it - see, for example, <a href="http://brainverse.repronim.org">BrainVerse</a>.
<li>Use a version control system for all files (data, code, environments, etc.) - i.e. <a href="http://datalad.org">DataLad</a>.
</ul>
</p>
<table style="width:100%;background-color:#b498d1;font-size:30px">
<tr>
<td><b>Data Processing</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/processing">repronim.org/5Steps/processing</a></td>
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<!-- <h2 style="background-color:#b498d1">Data Processing</h2> -->
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<li>Document your software and computational environment - for example <a href="https://github.com/kaczmarj/neurodocker">NeuroDocker</a> and <a href="http://niceman.repronim.org">NiceMan</a>.
<li>Use containerization/virtualization to encapsulate and share analysis workflow (<a href="http://docker.com">Docker</a>, <a href="https://www.sylabs.io/">Singularity</a>, <a href="https://www.virtualbox.org/">Virtual Machines</a>, etc.).
<li>Annotate your results - using NeuroImaging Data Model (<a href="http://nidm.nidash.org">NIDM</a>), for example.
</ul>
</p>
<table style="width:100%;background-color:#f3e0ff;font-size:30px">
<tr>
<td><b>Statistical Analysis</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/stats">repronim.org/5Steps/stats</a></td>
</tr>
</table>
<!-- <h2 style="background-color:#f3e0ff">Statistical Analysis</h2> -->
<p>
<ul type="square">
<li>Most studies are underpowered, combat this by sharing your data and reusing available data to enable creating larger data sets, thereby increasing study power. Understand:
<ul type="square">
<li>Effect size, confidence intervals, power, positive predictive value and significance testing - some training materials can be found <a href="http://www.reproducibleimaging.org/module-stats/">here</a>.
</ul>
</ul>
</p>
<table style="width:100%;background-color:#ffe09e;font-size:30px">
<tr>
<td><b>Publication</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/publication">repronim.org/5Steps/publication</a></td>
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<!-- <h2 style="background-color:#ffe09e">Publication Content</h2> -->
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<li>Include the anonymized raw data and workflow used - using resources such as <a href="https://zenodo.org/">zenodo</a>, etc.
<li>Include complete processed results
<li>Make it Findable, Accessible, Interoperable and Reusable (<a href="https://www.go-fair.org/fair-principles/">FAIR</a>)
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