make html

unravel/docs/_build/html/_modules/unravel/voxel_stats/vstats.html

@@ -358,6 +358,15 @@ <h1>Source code for unravel.voxel_stats.vstats</h1><div class="highlight"><pre>
 <span class="sd">------</span>
 <span class="sd">    vstats -mas mask.nii.gz -v</span>
 
+<span class="sd">Usage w/ additional options:</span>
+<span class="sd">----------------------------</span>
+<span class="sd">    vstats -mas mask.nii.gz -p 12000 -k 0 -op output_prefix -a atlas.nii.gz -v --options --seed=1</span>
+
+<span class="sd">Note:</span>
+<span class="sd">    - The --options flag is used to pass additional options to the randomise command.</span>
+<span class="sd">    - It should be the last flag specified in the command.</span>
+<span class="sd">    - The options should be specified as separate strings, e.g., --options --seed=1 -T</span>
+<span class="sd">    </span>
 <span class="sd">Prereqs: </span>
 <span class="sd">    - Input images from ``vstats_prep``, ``vstats_z_score``, or ``vstats_whole_to_avg``.</span>
 
@@ -389,10 +398,10 @@ <h1>Source code for unravel.voxel_stats.vstats</h1><div class="highlight"><pre>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-mas&#39;</span><span class="p">,</span> <span class="s1">&#39;--mask&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/mask.nii.gz&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;--permutations&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Number of permutations (divisible by 300). Default: 18000&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">18000</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-k&#39;</span><span class="p">,</span> <span class="s1">&#39;--kernel&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Smoothing kernel radius in mm if &gt; 0. Default: 0 &#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-opt&#39;</span><span class="p">,</span> <span class="s1">&#39;--options&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Additional options for randomise, specified like &quot;--seed=1 -T&quot;&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="p">[])</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-on&#39;</span><span class="p">,</span> <span class="s1">&#39;--output_prefix&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Prefix of output files. Default: current working dir name.&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz (Default: /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-op&#39;</span><span class="p">,</span> <span class="s1">&#39;--output_prefix&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Prefix of output files. Default: current working dir name.&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz (copied to stats/ for easier vizualization; Default: /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-opt&#39;</span><span class="p">,</span> <span class="s1">&#39;--options&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Additional options for randomise, specified like &quot;--seed=1 -T&quot;&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="n">argparse</span><span class="o">.</span><span class="n">REMAINDER</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="p">[])</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">epilog</span> <span class="o">=</span> <span class="vm">__doc__</span>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
 
@@ -507,10 +516,12 @@ <h1>Source code for unravel.voxel_stats.vstats</h1><div class="highlight"><pre>
     <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">atlas</span><span class="p">,</span> <span class="n">stats_dir</span><span class="p">)</span>
 
     <span class="c1"># Merge and smooth the input images</span>
-    <span class="n">images</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s1">&#39;*.nii.gz&#39;</span><span class="p">)</span> 
+    <span class="n">images</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">glob</span><span class="p">(</span><span class="s1">&#39;*.nii.gz&#39;</span><span class="p">))</span>
     <span class="n">merged_file</span> <span class="o">=</span> <span class="n">stats_dir</span> <span class="o">/</span> <span class="s1">&#39;all.nii.gz&#39;</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">merged_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">    Merging *.nii.gz into ./stats/all.nii.gz&#39;</span><span class="p">)</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">    Merging *.nii.gz into ./stats/all.nii.gz with this order of files:&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">image</span> <span class="ow">in</span> <span class="n">images</span><span class="p">:</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;    </span><span class="si">{</span><span class="n">image</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
         <span class="n">avwutils</span><span class="o">.</span><span class="n">fslmerge</span><span class="p">(</span><span class="s1">&#39;t&#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">merged_file</span><span class="p">),</span> <span class="o">*</span><span class="n">images</span><span class="p">)</span>
     <span class="k">else</span><span class="p">:</span> 
         <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">    ./stats/all.nii.gz exists. Skipping...</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>

unravel/docs/_build/html/unravel/toc.html

@@ -629,6 +629,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 </li>
 <li class="toctree-l2"><a class="reference internal" href="voxel_stats/vstats.html">unravel.voxel_stats.vstats module</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="voxel_stats/vstats.html#usage">Usage:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="voxel_stats/vstats.html#usage-w-additional-options">Usage w/ additional options:</a></li>
 <li class="toctree-l3"><a class="reference internal" href="voxel_stats/vstats.html#unravel.voxel_stats.vstats.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="voxel_stats/vstats.html#unravel.voxel_stats.vstats.check_fdr_command"><code class="docutils literal notranslate"><span class="pre">check_fdr_command()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="voxel_stats/vstats.html#unravel.voxel_stats.vstats.create_design_ttest2"><code class="docutils literal notranslate"><span class="pre">create_design_ttest2()</span></code></a></li>

unravel/docs/_build/html/unravel/voxel_stats/toc.html

@@ -530,6 +530,7 @@ <h1>unravel.voxel_stats package<a class="headerlink" href="#unravel-voxel-stats-
 </li>
 <li class="toctree-l1"><a class="reference internal" href="vstats.html">unravel.voxel_stats.vstats module</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="vstats.html#usage">Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="vstats.html#usage-w-additional-options">Usage w/ additional options:</a></li>
 <li class="toctree-l2"><a class="reference internal" href="vstats.html#unravel.voxel_stats.vstats.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="vstats.html#unravel.voxel_stats.vstats.check_fdr_command"><code class="docutils literal notranslate"><span class="pre">check_fdr_command()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="vstats.html#unravel.voxel_stats.vstats.create_design_ttest2"><code class="docutils literal notranslate"><span class="pre">create_design_ttest2()</span></code></a></li>

unravel/docs/_build/html/unravel/voxel_stats/vstats.html

@@ -494,6 +494,20 @@ <h2>Usage:<a class="headerlink" href="#usage" title="Link to this heading">#</a>
 <blockquote>
 <div><p>vstats -mas mask.nii.gz -v</p>
 </div></blockquote>
+</section>
+<section id="usage-w-additional-options">
+<h2>Usage w/ additional options:<a class="headerlink" href="#usage-w-additional-options" title="Link to this heading">#</a></h2>
+<blockquote>
+<div><p>vstats -mas mask.nii.gz -p 12000 -k 0 -op output_prefix -a atlas.nii.gz -v –options –seed=1</p>
+</div></blockquote>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<ul class="simple">
+<li><p>The –options flag is used to pass additional options to the randomise command.</p></li>
+<li><p>It should be the last flag specified in the command.</p></li>
+<li><p>The options should be specified as separate strings, e.g., –options –seed=1 -T</p></li>
+</ul>
+</div>
 <dl class="simple">
 <dt>Prereqs:</dt><dd><ul class="simple">
 <li><p>Input images from <code class="docutils literal notranslate"><span class="pre">vstats_prep</span></code>, <code class="docutils literal notranslate"><span class="pre">vstats_z_score</span></code>, or <code class="docutils literal notranslate"><span class="pre">vstats_whole_to_avg</span></code>.</p></li>
@@ -593,6 +607,7 @@ <h2>Usage:<a class="headerlink" href="#usage" title="Link to this heading">#</a>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage">Usage:</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage-w-additional-options">Usage w/ additional options:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.voxel_stats.vstats.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.voxel_stats.vstats.check_fdr_command"><code class="docutils literal notranslate"><span class="pre">check_fdr_command()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.voxel_stats.vstats.create_design_ttest2"><code class="docutils literal notranslate"><span class="pre">create_design_ttest2()</span></code></a></li>