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nx10 committed Aug 31, 2024
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6 changes: 3 additions & 3 deletions 1_welcome.html
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<title>The Styx Book</title>
<title>The Styx Book - Styx Book</title>


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<ol class="chapter"><li class="chapter-item expanded "><a href="1_welcome.html" class="active"><strong aria-hidden="true">1.</strong> The Styx Book</a></li><li class="chapter-item expanded "><a href="2_getting_started.html"><strong aria-hidden="true">2.</strong> Getting started</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="2a_installation.html"><strong aria-hidden="true">2.1.</strong> Installation</a></li><li class="chapter-item expanded "><a href="2b_runners.html"><strong aria-hidden="true">2.2.</strong> Runners</a></li><li class="chapter-item expanded "><a href="2c_tips_best_practices.html"><strong aria-hidden="true">2.3.</strong> Tips & best practices</a></li><li class="chapter-item expanded "><a href="2d_contributing_to_niwrap.html"><strong aria-hidden="true">2.4.</strong> Contributing to NiWrap</a></li></ol></li><li class="chapter-item expanded "><a href="3_getting_started.html"><strong aria-hidden="true">3.</strong> Advanced concepts</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="3a_custom_runners.html"><strong aria-hidden="true">3.1.</strong> Writing custom runners</a></li></ol></li></ol>
<ol class="chapter"><li class="chapter-item expanded "><a href="1_welcome.html" class="active"><strong aria-hidden="true">1.</strong> The Styx Book</a></li><li class="chapter-item expanded "><a href="2_getting_started.html"><strong aria-hidden="true">2.</strong> Getting started</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="2b_runners.html"><strong aria-hidden="true">2.1.</strong> Runners</a></li><li class="chapter-item expanded "><a href="2c_tips_best_practices.html"><strong aria-hidden="true">2.2.</strong> Tips & best practices</a></li><li class="chapter-item expanded "><a href="2d_contributing_to_niwrap.html"><strong aria-hidden="true">2.3.</strong> Contributing to NiWrap</a></li></ol></li><li class="chapter-item expanded "><a href="3_getting_started.html"><strong aria-hidden="true">3.</strong> Advanced concepts</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="3a_custom_runners.html"><strong aria-hidden="true">3.1.</strong> Writing custom runners</a></li></ol></li></ol>
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39 changes: 34 additions & 5 deletions 2_getting_started.html
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<head>
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<title>Getting started</title>
<title>Getting started - Styx Book</title>


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<nav id="sidebar" class="sidebar" aria-label="Table of contents">
<div class="sidebar-scrollbox">
<ol class="chapter"><li class="chapter-item expanded "><a href="1_welcome.html"><strong aria-hidden="true">1.</strong> The Styx Book</a></li><li class="chapter-item expanded "><a href="2_getting_started.html" class="active"><strong aria-hidden="true">2.</strong> Getting started</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="2a_installation.html"><strong aria-hidden="true">2.1.</strong> Installation</a></li><li class="chapter-item expanded "><a href="2b_runners.html"><strong aria-hidden="true">2.2.</strong> Runners</a></li><li class="chapter-item expanded "><a href="2c_tips_best_practices.html"><strong aria-hidden="true">2.3.</strong> Tips & best practices</a></li><li class="chapter-item expanded "><a href="2d_contributing_to_niwrap.html"><strong aria-hidden="true">2.4.</strong> Contributing to NiWrap</a></li></ol></li><li class="chapter-item expanded "><a href="3_getting_started.html"><strong aria-hidden="true">3.</strong> Advanced concepts</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="3a_custom_runners.html"><strong aria-hidden="true">3.1.</strong> Writing custom runners</a></li></ol></li></ol>
<ol class="chapter"><li class="chapter-item expanded "><a href="1_welcome.html"><strong aria-hidden="true">1.</strong> The Styx Book</a></li><li class="chapter-item expanded "><a href="2_getting_started.html" class="active"><strong aria-hidden="true">2.</strong> Getting started</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="2b_runners.html"><strong aria-hidden="true">2.1.</strong> Runners</a></li><li class="chapter-item expanded "><a href="2c_tips_best_practices.html"><strong aria-hidden="true">2.2.</strong> Tips & best practices</a></li><li class="chapter-item expanded "><a href="2d_contributing_to_niwrap.html"><strong aria-hidden="true">2.3.</strong> Contributing to NiWrap</a></li></ol></li><li class="chapter-item expanded "><a href="3_getting_started.html"><strong aria-hidden="true">3.</strong> Advanced concepts</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="3a_custom_runners.html"><strong aria-hidden="true">3.1.</strong> Writing custom runners</a></li></ol></li></ol>
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<h1 class="menu-title">Styx Book</h1>

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<a href="print.html" title="Print this book" aria-label="Print this book">
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<div id="content" class="content">
<main>
<h1 id="getting-started"><a class="header" href="#getting-started">Getting started</a></h1>
<blockquote>
<p>[!NOTE]<br />
This book uses Styx wrappers from the NiWrap package, but any Styx wrapper will work the same way.</p>
</blockquote>
<p>To get started install the <a href="https://github.com/childmindresearch/niwrap/tree/main">NiWrap</a> Python package:</p>
<pre><code class="language-sh">pip install -e "git+https://github.com/childmindresearch/niwrap.git/#egg=niwrap&amp;subdirectory=python"
</code></pre>
<p>From there on running commands will be as easy as:</p>
<pre><code class="language-Python">from niwrap import fsl

bet_output = fsl.bet(
infile="my_file.nii.gz",
binary_mask=True,
)
</code></pre>
<p>This runs the command</p>
<pre><code class="language-sh">bet my_file.nii.gz -m
</code></pre>
<p>and stores all the output files for easy access in <code>bet_output</code>.</p>
<p>These can then be used as an input to another Styx wrapper or with any other Python package like nilearn:</p>
<pre><code class="language-Python">from nilearn.plotting import plot_anat

plot_anat(bet_output.outfile)
</code></pre>
<blockquote>
<p>[!TIP]<br />
Styx includes detailed documentation about every command, argument, and output file. You should be able to just hover over any of them in your editor to view its documentation.</p>
</blockquote>
<p>The next chapter will explain how to use <em>Runners</em> to control how the commands get executed and intermediate files get stored.</p>

</main>

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