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day3.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>Course on Practical Neuroimaging in Python — Practical neuroimaging analysis</title>
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<div class="section" id="day-3-version-control-diagnostics">
<h1>Day 3: version control / diagnostics<a class="headerlink" href="#day-3-version-control-diagnostics" title="Permalink to this headline">¶</a></h1>
<p>3 / 6 / 2015</p>
<div class="section" id="reading">
<h2>Reading<a class="headerlink" href="#reading" title="Permalink to this headline">¶</a></h2>
<p>We are going to start getting used to the <a class="reference external" href="http://git-scm.com">git</a> version control system this
week.</p>
<p>Git is an essential tool for anyone using code and data, and you will find
yourself using this tool all the time, so it is important to invest time
learning how to use git.</p>
<p>To use git, it is very important to understand the basic ideas behind it.</p>
<p>So, please read the <a class="reference internal" href="git_parable.html"><span class="doc">The git parable</span></a> – an excellent introduction to the
ideas behind git. I’ve added some illustrations from <a class="reference download internal" href="_downloads/git_parable_johan_herland.pdf" download=""><code class="xref download docutils literal"><span class="pre">slides</span> <span class="pre">from</span> <span class="pre">a</span>
<span class="pre">talk</span> <span class="pre">by</span> <span class="pre">Johan</span> <span class="pre">Herland</span></code></a> – I did not add some
of the later slides to our local copy of the git parable page, but you may well find them
useful for illustrating the last few sections of the git parable.</p>
</div>
<div class="section" id="day">
<h2>Day<a class="headerlink" href="#day" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Loading data with nibabel;</p>
</li>
<li><p class="first">Four dimensions is space then time;</p>
</li>
<li><p class="first">Slicing over arbitrary dimensions (including time);</p>
</li>
<li><p class="first">Using boolean arrays for indexing;</p>
</li>
<li><p class="first">Python functions;</p>
</li>
<li><p class="first">Exercises:</p>
<blockquote>
<div><ul class="simple">
<li>standard deviation per volume;</li>
<li>making an <code class="docutils literal"><span class="pre">spm_global</span></code> function.</li>
</ul>
</div></blockquote>
</li>
<li><p class="first">Python modules and packages;</p>
</li>
<li><p class="first">Exercises:</p>
<blockquote>
<div><ul class="simple">
<li>make notebook code into self-contained module.</li>
</ul>
</div></blockquote>
</li>
<li><p class="first">Starting with version control;</p>
</li>
<li><p class="first">Make new git repository;</p>
</li>
<li><p class="first">Add module to git repository;</p>
</li>
<li><p class="first">Commit;</p>
</li>
</ul>
</div>
<div class="section" id="exercises">
<h2>Exercises<a class="headerlink" href="#exercises" title="Permalink to this headline">¶</a></h2>
<p>The usual instructions:</p>
<ul class="simple">
<li><code class="docutils literal"><span class="pre">cd</span> <span class="pre">pna/pna2015</span></code></li>
<li><code class="docutils literal"><span class="pre">git</span> <span class="pre">pull</span></code></li>
<li><code class="docutils literal"><span class="pre">cd</span> <span class="pre">day3</span></code></li>
<li><code class="docutils literal"><span class="pre">ipython</span> <span class="pre">notebook</span></code></li>
</ul>
<p>There is a web page listing of the exercise files at
<a class="reference external" href="https://github.com/practical-neuroimaging/pna2015/tree/master/day3">https://github.com/practical-neuroimaging/pna2015/tree/master/day3</a></p>
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<h3><a href="index.html">Table Of Contents</a></h3>
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<li><a class="reference internal" href="#">Day 3: version control / diagnostics</a><ul>
<li><a class="reference internal" href="#reading">Reading</a></li>
<li><a class="reference internal" href="#day">Day</a></li>
<li><a class="reference internal" href="#exercises">Exercises</a></li>
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</li>
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<h4>Previous topic</h4>
<p class="topless"><a href="day2.html"
title="previous chapter">Day 2: images as arrays and plotting</a></p>
<h4>Next topic</h4>
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title="next chapter">Day 4: first statistics / version control</a></p>
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>previous</a> |</li>
<big><big><big><li><a href="index.html">Home</a> | </li>
<li><a href="https://github.com/practical-neuroimaging/pna2015">Exercises</a> | </li>
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