sct-pipeline · PaulBautin · Mar 12, 2021 · Mar 12, 2021 · Mar 12, 2021 · Mar 13, 2021
diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
 ![csa-atrophy](https://github.com/sct-pipeline/csa-atrophy/blob/master/csa_atrophy_scheme3.png)
 
+[![Documentation Status](https://readthedocs.org/projects/sphinx/badge/?version=master)](https://csa-atrophy.readthedocs.io/en/latest/)
+
 # csa-atrophy
 
 Evaluate the sensitivity of atrophy detection with SCT. The algorithm works as follows:

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1 @@
+../README.md
diff --git a/docs/_build/doctrees/README.doctree b/docs/_build/doctrees/README.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/statistics.doctree b/docs/_build/doctrees/statistics.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 70aef56d01745b281df3c0294204b2b4
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/README.html b/docs/_build/html/README.html
@@ -0,0 +1,309 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8">
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+  <title>csa-atrophy &mdash; csa-atrophy v1.0 documentation</title>
+
+
+
+  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+
+
+
+
+
+
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+
+      <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
+        <script src="_static/doctools.js"></script>
+
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+
+
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="STATISTICS" href="statistics.html" />
+    <link rel="prev" title="Welcome to csa-atrophy’s documentation!" href="index.html" /> 
+</head>
+
+<body class="wy-body-for-nav">
+
+
+  <div class="wy-grid-for-nav">
+
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+            <a href="index.html" class="icon icon-home" alt="Documentation Home"> csa-atrophy
+
+
+
+          </a>
+
+
+
+
+
+
+
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+
+        </div>
+
+
+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+
+
+
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">csa-atrophy</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#how-to-run">How to run</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#quality-control">Quality Control</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#statistics">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">STATISTICS</a></li>
+</ul>
+
+
+
+        </div>
+
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+
+      <nav class="wy-nav-top" aria-label="top navigation">
+
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="index.html">csa-atrophy</a>
+
+      </nav>
+
+
+      <div class="wy-nav-content">
+
+        <div class="rst-content">
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+  <ul class="wy-breadcrumbs">
+
+      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
+
+      <li>csa-atrophy</li>
+
+
+      <li class="wy-breadcrumbs-aside">
+
+
+            <a href="_sources/README.md.txt" rel="nofollow"> View page source</a>
+
+
+      </li>
+
+  </ul>
+
+
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <p><img alt="csa-atrophy" src="https://github.com/sct-pipeline/csa-atrophy/blob/master/csa_atrophy_scheme3.png" /></p>
+<p><a class="reference external" href="https://csa-atrophy.readthedocs.io/en/latest/"><img alt="Documentation Status" src="https://readthedocs.org/projects/sphinx/badge/?version=master" /></a></p>
+<div class="section" id="csa-atrophy">
+<h1>csa-atrophy<a class="headerlink" href="#csa-atrophy" title="Permalink to this headline">¶</a></h1>
+<p>Evaluate the sensitivity of atrophy detection with SCT. The algorithm works as follows:</p>
+<ul class="simple">
+<li><p>Consider subject I –&gt; sI</p></li>
+<li><p>Applies a rescaling on the native image (e.g. 1, 0.95, 0.8) –&gt; rX</p></li>
+<li><p>Applies random affine transformation –&gt; tY</p></li>
+<li><p>Segment the cord</p></li>
+<li><p>Compute CSA –&gt; CSA(sI, rX, tY)</p></li>
+</ul>
+</div>
+<div class="section" id="how-to-run">
+<h1>How to run<a class="headerlink" href="#how-to-run" title="Permalink to this headline">¶</a></h1>
+<p>This code has been tested using Python 3.7.</p>
+<p>Download (or git clone) this repository:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">sct</span><span class="o">-</span><span class="n">pipeline</span><span class="o">/</span><span class="n">csa</span><span class="o">-</span><span class="n">atrophy</span><span class="o">.</span><span class="n">git</span>
+<span class="n">cd</span> <span class="n">csa</span><span class="o">-</span><span class="n">atrophy</span>
+</pre></div>
+</div>
+<p>Installation:
+csa-atrophy requires specific python packages for computing statistics and processing images. If not already present on the computer’s python environment such packages will automatically be installed by running pip command:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">e</span> <span class="o">.</span>
+</pre></div>
+</div>
+<p>Download the <a class="reference external" href="https://github.com/spine-generic/data-multi-subject#download">Spine Generic Multi-Subject dataset</a>.</p>
+<p>Edit the file <code class="docutils literal notranslate"><span class="pre">config_sct_run_batch.yml</span></code> according to your setup. Notable flags include:</p>
+<ul class="simple">
+<li><p><code class="docutils literal notranslate"><span class="pre">path_data</span></code>: If you downloaded the spine-generic data at another location, make sure to update the path;</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">include_list</span></code>: If you only want to run the script in a few subjects, list them here. Example:
+<code class="docutils literal notranslate"><span class="pre">include_list:</span> <span class="pre">['sub-unf04',</span> <span class="pre">'sub-unf05']</span></code></p></li>
+</ul>
+<p>See <code class="docutils literal notranslate"><span class="pre">sct_run_batch</span> <span class="pre">-h</span></code> to look at the available options.</p>
+<p>Run the analysis:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sct_run_batch</span> <span class="o">-</span><span class="n">config</span> <span class="n">config_sct_run_batch</span><span class="o">.</span><span class="n">yml</span>
+</pre></div>
+</div>
+<p>:note: <strong>desired subjects using flag -include and in parallel processing using flag -jobs.</strong></p>
+<p>To output statistics, run in Dataset</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">csa_rescale_stat</span> <span class="o">-</span><span class="n">i</span> <span class="n">csa_atrophy_results</span><span class="o">/</span><span class="n">results</span> <span class="o">-</span><span class="n">o</span> <span class="n">csa_atrophy_results</span> <span class="o">-</span><span class="n">config</span> <span class="n">config_script</span><span class="o">.</span><span class="n">yml</span> <span class="o">-</span><span class="n">fig</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="quality-control">
+<h1>Quality Control<a class="headerlink" href="#quality-control" title="Permalink to this headline">¶</a></h1>
+<p>After running the analysis, check your Quality Control (QC) report by opening the file qc/index.html. Use the
+“Search” feature of the QC report to quickly jump to segmentations or labeling results. If you spot issues
+(wrong labeling), add their filenames in the ‘config_correction.yml’ file
+(see https://spine-generic.rtfd.io/en/latest/analysis-pipeline.html for further indications). Then, manually create
+labels in the cord at the level of inter-vertebral discs C1-C2, C2-C3, …, C4-C5 with the command:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">manual_correction</span> <span class="o">-</span><span class="n">config</span> <span class="n">config_correction</span><span class="o">.</span><span class="n">yml</span> <span class="o">-</span><span class="n">path</span><span class="o">-</span><span class="ow">in</span> <span class="n">csa_atrophy_results</span><span class="o">/</span><span class="n">data_processed</span> <span class="o">-</span><span class="n">path</span><span class="o">-</span><span class="n">out</span> <span class="n">PATH_DATA</span>
+</pre></div>
+</div>
+<p>The bash script outputs all manual labelings to the derivatives directory in the dataset path defined in <code class="docutils literal notranslate"><span class="pre">path_data</span></code>.
+It is now possible to re-run the whole process. With the command below labeling will use the manual corrections that
+are present in the derivatives/ folder of the dataset, otherwise labeling will be done automatically.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sct_run_batch</span> <span class="o">-</span><span class="n">config</span> <span class="n">config_sct_run_batch</span><span class="o">.</span><span class="n">yml</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="statistics">
+<h1>Statistics<a class="headerlink" href="#statistics" title="Permalink to this headline">¶</a></h1>
+<p>After everything is done, compute stats:
+Per-subject stat: Panda dataframe <code class="docutils literal notranslate"><span class="pre">df_sub</span></code>:</p>
+<ul class="simple">
+<li><p>intra-subject MEAN: MEAN[CSA(sI, rX, :)] –&gt; MEAN_intra(sI, rX): <code class="docutils literal notranslate"><span class="pre">df_sub['mean']</span></code></p></li>
+<li><p>intra-subject STD: STD[CSA(sI, rX, :)] –&gt; STD_intra(sI, rX): <code class="docutils literal notranslate"><span class="pre">df_sub['std']</span></code></p></li>
+<li><p>intra-subject COV: STD[CSA(sI, rX, :)] / MEAN[CSA(sI, rX, :)] –&gt; COV_intra(sI, rX): <code class="docutils literal notranslate"><span class="pre">df_sub['cov']</span></code></p></li>
+<li><p>rescale_estimated_subject MEAN: MEAN[CSA(sI, rX, :) / CSA(sI, 1, :)] –&gt; MEAN_rescale_estimated_subject(sI, rX): <code class="docutils literal notranslate"><span class="pre">df_sub['rescale_estimated']</span></code></p></li>
+<li><p>intra-subject error MEAN: MEAN[CSA(sI, rX, :)] - (rX^2 * MEAN[CSA(sI, 1, :)]) –&gt; MEAN_error_intra(sI, rX): <code class="docutils literal notranslate"><span class="pre">df_sub['error']</span></code></p></li>
+<li><p>intra-subject error in percentage MEAN: [MEAN[CSA(sI, rX, :)] - (rX^2 * MEAN[CSA(sI, 1, :)])] / MEAN[CSA(sI, rX, :)] –&gt; MEAN_error_intra_perc(sI, rX): <code class="docutils literal notranslate"><span class="pre">df_sub['perc_error']</span></code></p></li>
+</ul>
+<p>Across-subject stats: Panda dataframe <code class="docutils literal notranslate"><span class="pre">df_rescale</span></code></p>
+<ul class="simple">
+<li><p>intra-subject STD: MEAN[STD_intra(:, rX)] –&gt; STD_intra(rX): <code class="docutils literal notranslate"><span class="pre">df_rescale['std_intra']</span></code></p></li>
+<li><p>intra-subject COV: MEAN[COV_intra_sub(:, rX)] –&gt; COV_intra(rX): <code class="docutils literal notranslate"><span class="pre">df_rescale['cov']</span></code></p></li>
+<li><p>inter-subject STD: STD[MEAN_intra(:, rX)] –&gt; STD_inter(rX): <code class="docutils literal notranslate"><span class="pre">df_rescale['std_inter']</span></code></p></li>
+<li><p>rescale_estimated (across subjects) MEAN: MEAN[MEAN_rescale_estimated_subject(:, rX)] –&gt; MEAN_rescale_estimated(rX): <code class="docutils literal notranslate"><span class="pre">df_rescale['mean_rescale_estimated']</span></code></p></li>
+<li><p>rescale_estimated (across subjects) STD: STD[MEAN_rescale_estimated_subject(:, rX)] –&gt; STD_rescale_estimated(rX): <code class="docutils literal notranslate"><span class="pre">df_rescale['std_rescale_estimated']</span></code></p></li>
+<li><p>error in percentage (across subjects) MEAN: MEAN[MEAN_error_intra(:, rX)]</p></li>
+<li><p>error in percentage (across subjects) STD: STD[MEAN_error_intra(:, rX)]</p></li>
+</ul>
+<p>Power analysis:</p>
+<ul class="simple">
+<li><p>sample size: [(z(uncertainty) + z(power))^2 * (2 * STD[MEAN(:, rX)]^2)] / [MEAN[CSA(sI, 1, :)] - MEAN[CSA(sI, rX, :)]]</p></li>
+</ul>
+<p>Plot results:</p>
+<ul class="simple">
+<li><p>STD_intersub</p></li>
+<li><p>Mean and STD inter-subject error percentage in function of rescaling</p></li>
+<li><p>sample size: minimum number of patients to detect an atrophy of X with Y% power and Z% uncertainty</p></li>
+<li><p>CSA values boxplot in function of rescaling</p></li>
+<li><p>Error values boxplot in function of rescaling</p></li>
+</ul>
+</div>
+
+
+           </div>
+
+          </div>
+          <footer>
+
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+
+        <a href="statistics.html" class="btn btn-neutral float-right" title="STATISTICS" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+
+
+        <a href="index.html" class="btn btn-neutral float-left" title="Welcome to csa-atrophy’s documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+
+    </div>
+
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+
+        &copy; Copyright 2021, Paul Bautin
+
+    </p>
+  </div>
+
+
+
+    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
+
+    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
+
+    provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+
+
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script>
+
+
+
+
+
+
+</body>
+</html>