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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<html xmlns="http://www.w3.org/1999/xhtml">
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<title>Course on Practical Neuroimaging in Python — Practical neuroimaging analysis</title>
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<div class="section" id="day-0-introduction-what-is-an-image">
<h1>Day 0 : introduction: what is an image?<a class="headerlink" href="#day-0-introduction-what-is-an-image" title="Permalink to this headline">¶</a></h1>
<p>February 13 2015</p>
<p>Download <a class="reference download internal" href="_downloads/day0_slides.pdf" download=""><code class="xref download docutils literal"><span class="pre">day0</span> <span class="pre">slides</span></code></a></p>
<div class="section" id="homework">
<h2>Homework<a class="headerlink" href="#homework" title="Permalink to this headline">¶</a></h2>
<p>Install requirements on your machine – see <a class="reference internal" href="installation.html"><span class="doc">Software to install for the class</span></a>.</p>
</div>
<div class="section" id="an-introduction-to-the-course">
<h2>An introduction to the course.<a class="headerlink" href="#an-introduction-to-the-course" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Replication crisis;</li>
<li>The ubiquity of error;</li>
<li>Scientists as coders;</li>
<li>Best practice;</li>
<li>The benefits of fluency;</li>
<li>Build your own light-sabre;</li>
<li>Simple first, then easy;</li>
<li>Why Python?;</li>
<li>Why git?</li>
<li>Your text editor.</li>
</ul>
</div>
<div class="section" id="admin-stuff">
<h2>Admin stuff<a class="headerlink" href="#admin-stuff" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Around 30 minutes homework;</p>
</li>
<li><p class="first">Homework ready by end of day Monday for following Friday course;</p>
</li>
<li><p class="first">Class consists of:</p>
<blockquote>
<div><ul class="simple">
<li>5 minute debrief from previous class;</li>
<li>30 minute talk and introduction to problems;</li>
<li>60 minutes working on problems;</li>
<li>10 minutes reviewing.</li>
</ul>
</div></blockquote>
</li>
<li><p class="first">Office hours;</p>
</li>
</ul>
</div>
<div class="section" id="introduction-to-the-exercises">
<h2>Introduction to the exercises<a class="headerlink" href="#introduction-to-the-exercises" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Open terminal (Mac, Linux) or Git Bash (Windows);</li>
<li>Make a directory <code class="docutils literal"><span class="pre">pna</span></code> with <code class="docutils literal"><span class="pre">mkdir</span> <span class="pre">pna</span></code>;</li>
<li>Change directory to <code class="docutils literal"><span class="pre">pna</span></code> with <code class="docutils literal"><span class="pre">cd</span> <span class="pre">pna</span></code>;</li>
<li><code class="docutils literal"><span class="pre">git</span> <span class="pre">clone</span> <span class="pre">git://github.com/practical-neuroimaging/pna2015.git</span></code></li>
<li><code class="docutils literal"><span class="pre">cd</span> <span class="pre">pna2015</span></code></li>
<li><code class="docutils literal"><span class="pre">ls</span></code></li>
</ul>
<p>You should see a directory listed called <code class="docutils literal"><span class="pre">day0</span></code>.</p>
<ul class="simple">
<li><code class="docutils literal"><span class="pre">cd</span> <span class="pre">day0</span></code></li>
<li>Start the IPython notebook with <code class="docutils literal"><span class="pre">ipython</span> <span class="pre">notebook</span></code></li>
<li>select and open “what_is_an_image” notebook.</li>
</ul>
</div>
<div class="section" id="references">
<h2>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><a class="reference external" href="http://nipyworld.blogspot.com/2012/04/replication-in-functional-mri.html">http://nipyworld.blogspot.com/2012/04/replication-in-functional-mri.html</a></li>
<li>Why most published research findings are false:
<a class="reference external" href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124">http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124</a></li>
<li><a class="reference external" href="http://python-history.blogspot.com/2013/10/why-python-uses-0-based-indexing.html">why Python uses 0-based indexing</a></li>
</ul>
</div>
<div class="section" id="quotes-from-david-donoho">
<h2>Quotes from David Donoho<a class="headerlink" href="#quotes-from-david-donoho" title="Permalink to this headline">¶</a></h2>
<p>Donoho quote 0:</p>
<blockquote>
<div>“The scientific method’s central motivation is the ubiquity of error –
the awareness that mistakes and self-delusion can creep in absolutely
anywhere and that the scientist’s effort is primarily expended in
recognizing and rooting out error.” <a class="reference internal" href="#donoho2009reproducible" id="id1">[donoho2009reproducible]</a></div></blockquote>
<p>Donoho quote 1:</p>
<blockquote>
<div>“In stark contrast to the sciences relying on deduction or empiricism,
computational science is far less visibly concerned with the ubiquity of
error. At conferences and in publications, it’s now completely acceptable
for a researcher to simply say, ‘here is what I did, and here are my
results.’ Presenters devote almost no time to explaining why the audience
should believe that they found and corrected errors in their computations.
The presentation’s core isn’t about the struggle to root out error — as it
would be in mature fields — but is instead a sales pitch: an enthusiastic
presentation of ideas and a breezy demo of an implementation. Computational
science has nothing like the elaborate mechanisms of formal proof in
mathematics or meta-analysis in empirical science. Many users of scientific
computing aren’t even trying to follow a systematic, rigorous discipline
that would in principle allow others to verify the claims they make. How
dare we imagine that computational science, as routinely practiced, is
reliable!” <a class="reference internal" href="#donoho2009reproducible" id="id2">[donoho2009reproducible]</a></div></blockquote>
<p>Donoho quote 2:</p>
<blockquote>
<div><p>“In my own experience, error is ubiquitous in scientific computing, and one
needs to work very diligently and energetically to eliminate it. One needs a
very clear idea of what has been done in order to know where to look for
likely sources of error. I often cannot really be sure what a student or
colleague has done from his/her own presentation, and in fact often his/her
description does not agree with my own understanding of what has been done,
once I look carefully at the scripts. Actually, I find that researchers
quite generally forget what they have done and misrepresent their
computations.</p>
<p>Computing results are now being presented in a very loose, “breezy” way—in
journal articles, in conferences, and in books. All too often one simply
takes computations at face value. This is spectacularly against the evidence
of my own experience. I would much rather that at talks and in referee
reports, the possibility of such error were seriously examined.”
<a class="reference internal" href="#donoho2010invitation" id="id3">[donoho2010invitation]</a></p>
</div></blockquote>
<table class="docutils citation" frame="void" id="donoho2009reproducible" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label">[donoho2009reproducible]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>)</em> Donoho, David L, et al. 2009. Reproducible research in computational
harmonic analysis. <em>Computing in Science & Engineering</em> 11, 8–18.
<a class="reference external" href="http://www.stanford.edu/~vcs/papers/ReproducibleResearch20080811.pdf">http://www.stanford.edu/~vcs/papers/ReproducibleResearch20080811.pdf</a></td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="donoho2010invitation" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id3">[donoho2010invitation]</a></td><td>Donoho, David L. 2010. An invitation to reproducible
computational research. <em>Biostatistics</em> 11, 385–388.
<a class="reference external" href="http://biostatistics.oxfordjournals.org/content/11/3/385.full">http://biostatistics.oxfordjournals.org/content/11/3/385.full</a></td></tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Day 0 : introduction: what is an image?</a><ul>
<li><a class="reference internal" href="#homework">Homework</a></li>
<li><a class="reference internal" href="#an-introduction-to-the-course">An introduction to the course.</a></li>
<li><a class="reference internal" href="#admin-stuff">Admin stuff</a></li>
<li><a class="reference internal" href="#introduction-to-the-exercises">Introduction to the exercises</a></li>
<li><a class="reference internal" href="#references">References</a></li>
<li><a class="reference internal" href="#quotes-from-david-donoho">Quotes from David Donoho</a></li>
</ul>
</li>
</ul>
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