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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-9-optimization-2d-interpolation-and-registration">
<h1>Day 9: optimization, 2D interpolation and registration<a class="headerlink" href="#day-9-optimization-2d-interpolation-and-registration" title="Permalink to this headline">¶</a></h1>
<p>4 / 24 / 2015</p>
<div class="section" id="reading">
<h2>Reading<a class="headerlink" href="#reading" title="Permalink to this headline">¶</a></h2>
<p>The reading for this weeks class is a notebook in the <cite>pna2015</cite> repository:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">pna2015</span>
<span class="n">git</span> <span class="n">pull</span>
<span class="n">ipython</span> <span class="n">notebook</span>
</pre></div>
</div>
<p>The main notebook is <code class="docutils literal"><span class="pre">day9/optimizing_space.ipynb</span></code> - but you’ll see a couple
of other notebooks there that the main notebook links to.</p>
<p>Here are the notebooks generated as non-interactive web pages, for reference:</p>
<ul class="simple">
<li><a class="reference external" href="http://nbviewer.ipython.org/github/practical-neuroimaging/pna2015/blob/master/day9/optimizing_space.ipynb">main notebook on spatial registration</a>;</li>
<li><a class="reference external" href="http://nbviewer.ipython.org/github/practical-neuroimaging/pna2015/blob/master/day9/functions_are_objects.ipynb">background on Python functions</a>;</li>
<li><a class="reference external" href="http://nbviewer.ipython.org/github/practical-neuroimaging/pna2015/blob/master/day9/global_scope.ipynb">background on global variable scope</a>.</li>
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<p>You may also want to have a look at <a class="reference internal" href="rotation_2d.html"><span class="doc">Formula for rotating a vector in 2D</span></a>.</p>
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<div class="section" id="day">
<h2>Day<a class="headerlink" href="#day" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Convert optimization notebook to Python module;</li>
<li>Run;</li>
<li>Try different cost functions;</li>
<li>Try different optimization methods;</li>
<li>Local minima with a 180 degree rotation;</li>
<li>Investigate and run FSL motion correction.</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">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/day9">https://github.com/practical-neuroimaging/pna2015/tree/master/day9</a></p>
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<li><a class="reference internal" href="#">Day 9: optimization, 2D interpolation and registration</a><ul>
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<li><a class="reference internal" href="#day">Day</a></li>
<li><a class="reference internal" href="#exercises">Exercises</a></li>
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<p class="topless"><a href="day8.html"
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title="next chapter">Day 10: coordinate systems and cross-modality registration</a></p>
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