deploy: 563376d

dev/Authors.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Citations" href="Citations.html" /><link rel="prev" title="Changelog" href="Changelog.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Authors - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -333,7 +333,7 @@ <h1>Authors<a class="headerlink" href="#authors" title="Link to this heading">¶
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Changelog.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Authors" href="Authors.html" /><link rel="prev" title="Requirements" href="Requirements.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Changelog - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -377,7 +377,7 @@ <h2>Version 2.0.0<a class="headerlink" href="#version-2-0-0" title="Link to this
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Citations.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="License" href="License.html" /><link rel="prev" title="Authors" href="Authors.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Citations - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -334,7 +334,7 @@ <h1>Citations<a class="headerlink" href="#citations" title="Link to this heading
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Development.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Usage" href="Usage.html" /><link rel="prev" title="Functionality" href="Functionality.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Development - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -365,7 +365,7 @@ <h2>Roadmap<a class="headerlink" href="#roadmap" title="Link to this heading">¶
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Functionality.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Development" href="Development.html" /><link rel="prev" title="Welcome to fsqc’s documentation!" href="index.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Functionality - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -473,7 +473,7 @@ <h2>outlier module<a class="headerlink" href="#outlier-module" title="Link to th
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Installation.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Requirements" href="Requirements.html" /><link rel="prev" title="Usage" href="Usage.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Installation - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -385,7 +385,7 @@ <h2>Download from GitHub<a class="headerlink" href="#download-from-github" title
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/License.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="API References" href="api/index.html" /><link rel="prev" title="Citations" href="Citations.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>License - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -330,7 +330,7 @@ <h1>License<a class="headerlink" href="#license" title="Link to this heading">¶
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Requirements.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Changelog" href="Changelog.html" /><link rel="prev" title="Installation" href="Installation.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Requirements - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -273,15 +273,15 @@ <h1>Requirements<a class="headerlink" href="#requirements" title="Link to this h
 <ul>
 <li><p>At least one structural MR image that was processed with Freesurfer 6.0, 7.x, or FastSurfer 1.1 or later (including the surface pipeline).</p></li>
 <li><p>A Python version &gt;= 3.8 is required to run this script.</p></li>
-<li><p>Required packages include (among others) the <code class="xref py py-obj docutils literal notranslate"><span class="pre">nibabel</span></code> and <code class="xref py py-obj docutils literal notranslate"><span class="pre">skimage</span></code> packages for the core functionality, plus the <a class="reference external" href="https://matplotlib.org/stable/index.html#module-matplotlib" title="(in Matplotlib v3.9.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matplotlib</span></code></a>, <a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/index.html#module-pandas" title="(in pandas v2.2.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas</span></code></a>, and <code class="xref py py-obj docutils literal notranslate"><span class="pre">transform3d</span></code> packages for some optional functions and modules. See the <code class="xref py py-obj docutils literal notranslate"><span class="pre">requirements.txt</span></code> file for a complete list.
+<li><p>Required packages include (among others) the <code class="xref py py-obj docutils literal notranslate"><span class="pre">nibabel</span></code> and <code class="xref py py-obj docutils literal notranslate"><span class="pre">skimage</span></code> packages for the core functionality, plus the <a class="reference external" href="https://matplotlib.org/stable/index.html#module-matplotlib" title="(in Matplotlib v3.9.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matplotlib</span></code></a>, <a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/index.html#module-pandas" title="(in pandas v2.2.3)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas</span></code></a>, and <code class="xref py py-obj docutils literal notranslate"><span class="pre">transform3d</span></code> packages for some optional functions and modules. See the <code class="xref py py-obj docutils literal notranslate"><span class="pre">requirements.txt</span></code> file for a complete list.
 Use the following command to install these packages:</p>
 <p><code class="docutils literal notranslate"><span class="pre">`</span>
 <span class="pre">bash</span>
 <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">-r</span> <span class="pre">requirements.txt</span>
 <span class="pre">`</span></code></p>
 </li>
 <li><p>If installing the toolbox as a Python package or if using the Docker image, all required packages will be installed automatically, and manual installation as detailed above will not be necessary.</p></li>
-<li><p>This software has been tested on Ubuntu 20.04.</p></li>
+<li><p>This software has been tested on Ubuntu 20.04 and Ubuntu 22.04.</p></li>
 <li><p>A working <a class="reference external" href="https://freesurfer.net/">FreeSurfer</a> installation (version 6 or newer) is required for running the ‘shape’ module of this toolbox. Also, make sure that FreeSurfer is sourced (i.e., FREESURFER_HOME is set as an environment variable) before running an analysis.</p></li>
 </ul>
 <section id="known-issues">
@@ -367,7 +367,7 @@ <h2>Known issues<a class="headerlink" href="#known-issues" title="Link to this h
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>

dev/Usage.html

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Installation" href="Installation.html" /><link rel="prev" title="Development" href="Development.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
         <title>Usage - fsqc</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
@@ -275,14 +275,16 @@ <h2>As a Command Line Tool<a class="headerlink" href="#as-a-command-line-tool" t
 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>run_fsqc
 --subjects_dir<span class="w"> </span>&lt;directory&gt;
 --output_dir<span class="w"> </span>&lt;directory&gt;
-<span class="o">[</span>--subjects<span class="w"> </span>SubjectID<span class="o">]</span>
+<span class="o">[</span>--subjects<span class="w"> </span>SubjectID<span class="w"> </span><span class="o">[</span>SubjectID<span class="w"> </span>...<span class="o">]]</span>
 <span class="o">[</span>--subjects-file<span class="w"> </span>&lt;file&gt;<span class="o">]</span><span class="w"> </span><span class="o">[</span>--screenshots<span class="o">]</span>
 <span class="o">[</span>--screenshots-html<span class="o">]</span><span class="w"> </span><span class="o">[</span>--surfaces<span class="o">]</span><span class="w"> </span><span class="o">[</span>--surfaces-html<span class="o">]</span>
 <span class="o">[</span>--skullstrip<span class="o">]</span><span class="w"> </span><span class="o">[</span>--skullstrip-html<span class="o">]</span>
 <span class="o">[</span>--fornix<span class="o">]</span><span class="w"> </span><span class="o">[</span>--fornix-html<span class="o">]</span><span class="w"> </span><span class="o">[</span>--hippocampus<span class="o">]</span>
 <span class="o">[</span>--hippocampus-html<span class="o">]</span><span class="w"> </span><span class="o">[</span>--hippocampus-label<span class="w"> </span>...<span class="w"> </span><span class="o">]</span>
 <span class="o">[</span>--hypothalamus<span class="o">]</span><span class="w"> </span><span class="o">[</span>--hypothalamus-html<span class="o">]</span><span class="w"> </span><span class="o">[</span>--shape<span class="o">]</span>
-<span class="o">[</span>--outlier<span class="o">]</span><span class="w"> </span><span class="o">[</span>--fastsurfer<span class="o">]</span><span class="w"> </span><span class="o">[</span>-h<span class="o">]</span><span class="w"> </span><span class="o">[</span>--more-help<span class="o">]</span>
+<span class="o">[</span>--outlier<span class="o">]</span><span class="w"> </span><span class="o">[</span>--fastsurfer<span class="o">]</span><span class="w"> </span><span class="o">[</span>--no-group<span class="o">]</span>
+<span class="o">[</span>--group-only<span class="o">]</span><span class="w"> </span><span class="o">[</span>--exit-on-error<span class="o">]</span>
+<span class="o">[</span>--skip-existing<span class="o">]</span><span class="w"> </span><span class="o">[</span>-h<span class="o">]</span><span class="w"> </span><span class="o">[</span>--more-help<span class="o">]</span>
 <span class="o">[</span>...<span class="o">]</span>
 
 Required<span class="w"> </span>Arguments:
@@ -354,9 +356,18 @@ <h2>As a Command Line Tool<a class="headerlink" href="#as-a-command-line-tool" t
 --fastsurfer
 <span class="w">    </span>Use<span class="w"> </span>FastSurfer<span class="w"> </span>instead<span class="w"> </span>of<span class="w"> </span>FreeSurfer<span class="w"> </span>output
 
+--no-group
+<span class="w">    </span>run<span class="w"> </span>script<span class="w"> </span><span class="k">in</span><span class="w"> </span>subject-level<span class="w"> </span>mode.<span class="w"> </span>will<span class="w"> </span>compute<span class="w"> </span>individual<span class="w"> </span>files<span class="w"> </span>and<span class="w"> </span>statistics,<span class="w"> </span>but<span class="w"> </span>not<span class="w"> </span>create<span class="w"> </span>group-level<span class="w"> </span>summaries.
+
+--group-only
+<span class="w">    </span>run<span class="w"> </span>script<span class="w"> </span><span class="k">in</span><span class="w"> </span>group<span class="w"> </span>mode.<span class="w"> </span>will<span class="w"> </span>create<span class="w"> </span>group-level<span class="w"> </span>summaries<span class="w"> </span>from<span class="w"> </span>existing<span class="w"> </span>inputs.<span class="w"> </span>needs<span class="w"> </span>to<span class="w"> </span>be<span class="w"> </span>run<span class="w"> </span>on<span class="w"> </span>output<span class="w"> </span>directory<span class="w"> </span>with<span class="w"> </span>already<span class="w"> </span>existing<span class="w"> </span>results.
+
 --exit-on-error
 <span class="w">    </span>Terminate<span class="w"> </span>the<span class="w"> </span>program<span class="w"> </span>when<span class="w"> </span>encountering<span class="w"> </span>an<span class="w"> </span>error<span class="p">;</span><span class="w"> </span>otherwise,<span class="w"> </span>try<span class="w"> </span>to<span class="w"> </span><span class="k">continue</span><span class="w"> </span>with<span class="w"> </span>the<span class="w"> </span>next<span class="w"> </span>module<span class="w"> </span>or<span class="w"> </span><span class="k">case</span>
 
+--skip-existing
+<span class="w">    </span>skips<span class="w"> </span>processing<span class="w"> </span><span class="k">for</span><span class="w"> </span>a<span class="w"> </span>given<span class="w"> </span><span class="k">case</span><span class="w"> </span><span class="k">if</span><span class="w"> </span>output<span class="w"> </span>already<span class="w"> </span>exists,<span class="w"> </span>even<span class="w"> </span>with<span class="w"> </span>possibly<span class="w"> </span>different<span class="w"> </span>parameters<span class="w"> </span>or<span class="w"> </span>settings
+
 Getting<span class="w"> </span>Help:
 -------------
 -h,<span class="w"> </span>--help
@@ -546,7 +557,7 @@ <h2>As a Docker Image<a class="headerlink" href="#as-a-docker-image" title="Link
     </aside>
   </div>
 </div><script src="_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=5fa4622c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>