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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Course on Practical Neuroimaging in Python — Practical neuroimaging analysis</title>
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<div class="section" id="day-4-first-statistics-version-control">
<h1>Day 4: first statistics / version control<a class="headerlink" href="#day-4-first-statistics-version-control" title="Permalink to this headline">¶</a></h1>
<p>3 / 13 / 2015</p>
<div class="section" id="reading">
<h2>Reading<a class="headerlink" href="#reading" title="Permalink to this headline">¶</a></h2>
<p>We finish our git introduction with two short videos:</p>
<iframe src="https://player.vimeo.com/video/121579300" width="500"
height="342" frameborder="0" webkitallowfullscreen mozallowfullscreen
allowfullscreen></iframe> <p><a
href="https://vimeo.com/121579300">Introduction to the git working tree,
repository and staging area</a> (18 minutes).</p>
<iframe src="https://player.vimeo.com/video/121579601" width="500"
height="341" frameborder="0" webkitallowfullscreen mozallowfullscreen
allowfullscreen></iframe> <p><a href="https://vimeo.com/121579601">The
links between git commits, and git branches</a> (9 minutes).</p></div>
<div class="section" id="day">
<h2>Day<a class="headerlink" href="#day" title="Permalink to this headline">¶</a></h2>
<div class="section" id="getting-started-with-version-control">
<h3>Getting started with version control<a class="headerlink" href="#getting-started-with-version-control" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li>Starting with version control;</li>
<li>Make new git repository;</li>
<li>Add module to git repository;</li>
<li>Commit;</li>
</ul>
</div>
<div class="section" id="on-the-python-path">
<h3>On the Python path<a class="headerlink" href="#on-the-python-path" title="Permalink to this headline">¶</a></h3>
<p>See <a class="reference internal" href="python_path.html"><span class="doc">Putting modules on the Python path</span></a>.</p>
</div>
<div class="section" id="our-first-pass-at-fmri-statistics">
<h3>Our first pass at FMRI statistics<a class="headerlink" href="#our-first-pass-at-fmri-statistics" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li>Splitting FMRI time series by slicing;</li>
<li>Subtracting on blocks from off blocks;</li>
<li>Removing artefacts;</li>
<li>Visualizing results.</li>
</ul>
</div>
</div>
<div class="section" id="exercises">
<h2>Exercises<a class="headerlink" href="#exercises" title="Permalink to this headline">¶</a></h2>
<p>We start with a type-along session with git.</p>
<p>Then we go on to 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">day4</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/day4">https://github.com/practical-neuroimaging/pna2015/tree/master/day4</a></p>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Day 4: first statistics / version control</a><ul>
<li><a class="reference internal" href="#reading">Reading</a></li>
<li><a class="reference internal" href="#day">Day</a><ul>
<li><a class="reference internal" href="#getting-started-with-version-control">Getting started with version control</a></li>
<li><a class="reference internal" href="#on-the-python-path">On the Python path</a></li>
<li><a class="reference internal" href="#our-first-pass-at-fmri-statistics">Our first pass at FMRI statistics</a></li>
</ul>
</li>
<li><a class="reference internal" href="#exercises">Exercises</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="day3.html"
title="previous chapter">Day 3: version control / diagnostics</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="day5.html"
title="next chapter">Day 5: convolution and correlation</a></p>
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<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="day5.html" title="Day 5: convolution and correlation"
>next</a> |</li>
<li class="right" >
<a href="day3.html" title="Day 3: version control / diagnostics"
>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>
<li><a href="https://calmail.berkeley.edu/manage/list/listinfo/practical_fmri@lists.berkeley.edu">Mailing list</a> | </li></big></big></big>
<li class="nav-item nav-item-1"><a href="schedule.html" >Schedule</a> »</li>
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