make html

unravel/docs/_build/html/_modules/index.html

@@ -419,6 +419,8 @@ <h1>All modules for which code is available</h1>
 <li><a href="unravel/voxel_stats/apply_mask.html">unravel.voxel_stats.apply_mask</a></li>
 <li><a href="unravel/voxel_stats/hemi_to_LR_avg.html">unravel.voxel_stats.hemi_to_LR_avg</a></li>
 <li><a href="unravel/voxel_stats/mirror.html">unravel.voxel_stats.mirror</a></li>
+<li><a href="unravel/voxel_stats/other/IF_outliers.html">unravel.voxel_stats.other.IF_outliers</a></li>
+<li><a href="unravel/voxel_stats/other/r_to_p.html">unravel.voxel_stats.other.r_to_p</a></li>
 <li><a href="unravel/voxel_stats/vstats.html">unravel.voxel_stats.vstats</a></li>
 <li><a href="unravel/voxel_stats/vstats_prep.html">unravel.voxel_stats.vstats_prep</a></li>
 <li><a href="unravel/voxel_stats/whole_to_LR_avg.html">unravel.voxel_stats.whole_to_LR_avg</a></li>

unravel/docs/_build/html/_sources/guide.md.txt

@@ -226,7 +226,7 @@ unravel_commands -m
 
 :::{tab-item} Utilities
 - [**utils_agg_files**](unravel.utilities.aggregate_files_from_sample_dirs): Aggregate files from sample directories.
-- [**utils_agg_files_rec**](unravel.utilities.aggregate_files_w_recursive_search): Recursively aggregate files.
+- [**utils_agg_files_rec**](unravel.utilities.aggregate_files_recursively): Recursively aggregate files.
 - [**utils_prepend**](unravel.utilities.prepend_conditions): Prepend conditions to files using sample_key.csv.
 - [**utils_rename**](unravel.utilities.rename): Rename files.
 - [**utils_toggle**](unravel.utilities.toggle_samples): Toggle sample?? folders for select batch processing.

unravel/docs/_build/html/genindex.html

@@ -474,10 +474,12 @@ <h2 id="D">D</h2>
       <li><a href="unravel/image_io/zarr_to_nii.html#unravel.image_io.zarr_to_nii.define_zarr_to_nii_output">define_zarr_to_nii_output() (in module unravel.image_io.zarr_to_nii)</a>
 </li>
       <li><a href="unravel/cluster_stats/cluster_validation.html#unravel.cluster_stats.cluster_validation.density_in_cluster">density_in_cluster() (in module unravel.cluster_stats.cluster_validation)</a>
+</li>
+      <li><a href="unravel/cluster_stats/cluster_validation.html#unravel.cluster_stats.cluster_validation.density_in_cluster_parallel">density_in_cluster_parallel() (in module unravel.cluster_stats.cluster_validation)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="unravel/cluster_stats/cluster_validation.html#unravel.cluster_stats.cluster_validation.density_in_cluster_parallel">density_in_cluster_parallel() (in module unravel.cluster_stats.cluster_validation)</a>
+      <li><a href="unravel/voxel_stats/other/IF_outliers.html#unravel.voxel_stats.other.IF_outliers.detect_outliers">detect_outliers() (in module unravel.voxel_stats.other.IF_outliers)</a>
 </li>
       <li><a href="unravel/image_tools/DoG.html#unravel.image_tools.DoG.difference_of_gaussians">difference_of_gaussians() (in module unravel.image_tools.DoG)</a>
 </li>
@@ -787,6 +789,10 @@ <h2 id="M">M</h2>
         <li><a href="unravel/voxel_stats/hemi_to_LR_avg.html#unravel.voxel_stats.hemi_to_LR_avg.main">(in module unravel.voxel_stats.hemi_to_LR_avg)</a>
 </li>
         <li><a href="unravel/voxel_stats/mirror.html#unravel.voxel_stats.mirror.main">(in module unravel.voxel_stats.mirror)</a>
+</li>
+        <li><a href="unravel/voxel_stats/other/IF_outliers.html#unravel.voxel_stats.other.IF_outliers.main">(in module unravel.voxel_stats.other.IF_outliers)</a>
+</li>
+        <li><a href="unravel/voxel_stats/other/r_to_p.html#unravel.voxel_stats.other.r_to_p.main">(in module unravel.voxel_stats.other.r_to_p)</a>
 </li>
         <li><a href="unravel/voxel_stats/vstats.html#unravel.voxel_stats.vstats.main">(in module unravel.voxel_stats.vstats)</a>
 </li>
@@ -804,6 +810,8 @@ <h2 id="M">M</h2>
 </li>
       </ul></li>
       <li><a href="unravel/voxel_stats/apply_mask.html#unravel.voxel_stats.apply_mask.mean_intensity_in_brain">mean_intensity_in_brain() (in module unravel.voxel_stats.apply_mask)</a>
+</li>
+      <li><a href="unravel/voxel_stats/other/IF_outliers.html#unravel.voxel_stats.other.IF_outliers.mean_intensity_within_mask">mean_intensity_within_mask() (in module unravel.voxel_stats.other.IF_outliers)</a>
 </li>
       <li><a href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html#unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative.mean_std_count">mean_std_count() (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative)</a>
 </li>
@@ -966,6 +974,10 @@ <h2 id="M">M</h2>
         <li><a href="unravel/voxel_stats/hemi_to_LR_avg.html#module-unravel.voxel_stats.hemi_to_LR_avg">unravel.voxel_stats.hemi_to_LR_avg</a>
 </li>
         <li><a href="unravel/voxel_stats/mirror.html#module-unravel.voxel_stats.mirror">unravel.voxel_stats.mirror</a>
+</li>
+        <li><a href="unravel/voxel_stats/other/IF_outliers.html#module-unravel.voxel_stats.other.IF_outliers">unravel.voxel_stats.other.IF_outliers</a>
+</li>
+        <li><a href="unravel/voxel_stats/other/r_to_p.html#module-unravel.voxel_stats.other.r_to_p">unravel.voxel_stats.other.r_to_p</a>
 </li>
         <li><a href="unravel/voxel_stats/vstats.html#module-unravel.voxel_stats.vstats">unravel.voxel_stats.vstats</a>
 </li>
@@ -1146,6 +1158,10 @@ <h2 id="P">P</h2>
         <li><a href="unravel/voxel_stats/hemi_to_LR_avg.html#unravel.voxel_stats.hemi_to_LR_avg.parse_args">(in module unravel.voxel_stats.hemi_to_LR_avg)</a>
 </li>
         <li><a href="unravel/voxel_stats/mirror.html#unravel.voxel_stats.mirror.parse_args">(in module unravel.voxel_stats.mirror)</a>
+</li>
+        <li><a href="unravel/voxel_stats/other/IF_outliers.html#unravel.voxel_stats.other.IF_outliers.parse_args">(in module unravel.voxel_stats.other.IF_outliers)</a>
+</li>
+        <li><a href="unravel/voxel_stats/other/r_to_p.html#unravel.voxel_stats.other.r_to_p.parse_args">(in module unravel.voxel_stats.other.r_to_p)</a>
 </li>
         <li><a href="unravel/voxel_stats/vstats.html#unravel.voxel_stats.vstats.parse_args">(in module unravel.voxel_stats.vstats)</a>
 </li>
@@ -1196,6 +1212,8 @@ <h2 id="P">P</h2>
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="unravel/voxel_stats/other/r_to_p.html#unravel.voxel_stats.other.r_to_p.r_to_z">r_to_z() (in module unravel.voxel_stats.other.r_to_p)</a>
+</li>
       <li><a href="unravel/register/reg_prep.html#unravel.register.reg_prep.reg_prep">reg_prep() (in module unravel.register.reg_prep)</a>
 </li>
       <li><a href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html#unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative.relative_hedges_g">relative_hedges_g() (in module unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative)</a>
@@ -1626,15 +1644,15 @@ <h2 id="U">U</h2>
         <li><a href="unravel/image_tools/atlas/wireframe.html#module-unravel.image_tools.atlas.wireframe">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     unravel.image_tools.avg
 
       <ul>
         <li><a href="unravel/image_tools/avg.html#module-unravel.image_tools.avg">module</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     unravel.image_tools.bbox
 
@@ -1857,6 +1875,20 @@ <h2 id="U">U</h2>
 
       <ul>
         <li><a href="unravel/voxel_stats/mirror.html#module-unravel.voxel_stats.mirror">module</a>
+</li>
+      </ul></li>
+      <li>
+    unravel.voxel_stats.other.IF_outliers
+
+      <ul>
+        <li><a href="unravel/voxel_stats/other/IF_outliers.html#module-unravel.voxel_stats.other.IF_outliers">module</a>
+</li>
+      </ul></li>
+      <li>
+    unravel.voxel_stats.other.r_to_p
+
+      <ul>
+        <li><a href="unravel/voxel_stats/other/r_to_p.html#module-unravel.voxel_stats.other.r_to_p">module</a>
 </li>
       </ul></li>
       <li>
@@ -1952,6 +1984,8 @@ <h2 id="Z">Z</h2>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="unravel/voxel_stats/other/r_to_p.html#unravel.voxel_stats.other.r_to_p.z_to_p">z_to_p() (in module unravel.voxel_stats.other.r_to_p)</a>
+</li>
       <li><a href="unravel/image_io/zarr_to_nii.html#unravel.image_io.zarr_to_nii.zarr_to_ndarray">zarr_to_ndarray() (in module unravel.image_io.zarr_to_nii)</a>
 </li>
   </ul></td>

unravel/docs/_build/html/guide.html

@@ -640,7 +640,7 @@ <h2>Common commands<a class="headerlink" href="#common-commands" title="Link to
 Utilities</label><div class="sd-tab-content docutils">
 <ul class="simple">
 <li><p><a class="reference internal" href="unravel/utilities/aggregate_files_from_sample_dirs.html#unravel-utilities-aggregate-files-from-sample-dirs"><span class="std std-ref"><strong>utils_agg_files</strong></span></a>: Aggregate files from sample directories.</p></li>
-<li><p><a class="reference internal" href="#unravel.utilities.aggregate_files_w_recursive_search"><span class="xref myst"><strong>utils_agg_files_rec</strong></span></a>: Recursively aggregate files.</p></li>
+<li><p><a class="reference internal" href="unravel/utilities/aggregate_files_recursively.html#unravel-utilities-aggregate-files-recursively"><span class="std std-ref"><strong>utils_agg_files_rec</strong></span></a>: Recursively aggregate files.</p></li>
 <li><p><a class="reference internal" href="unravel/utilities/prepend_conditions.html#unravel-utilities-prepend-conditions"><span class="std std-ref"><strong>utils_prepend</strong></span></a>: Prepend conditions to files using sample_key.csv.</p></li>
 <li><p><a class="reference internal" href="unravel/utilities/rename.html#unravel-utilities-rename"><span class="std std-ref"><strong>utils_rename</strong></span></a>: Rename files.</p></li>
 <li><p><a class="reference internal" href="unravel/utilities/toggle_samples.html#unravel-utilities-toggle-samples"><span class="std std-ref"><strong>utils_toggle</strong></span></a>: Toggle sample?? folders for select batch processing.</p></li>

unravel/docs/_build/html/py-modindex.html

@@ -704,6 +704,16 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="unravel/voxel_stats/mirror.html#module-unravel.voxel_stats.mirror"><code class="xref">unravel.voxel_stats.mirror</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="unravel/voxel_stats/other/IF_outliers.html#module-unravel.voxel_stats.other.IF_outliers"><code class="xref">unravel.voxel_stats.other.IF_outliers</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="unravel/voxel_stats/other/r_to_p.html#module-unravel.voxel_stats.other.r_to_p"><code class="xref">unravel.voxel_stats.other.r_to_p</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;

unravel/docs/_build/html/unravel/voxel_stats/other/IF_outliers.html

@@ -491,8 +491,35 @@
 <div id="searchbox"></div>
                 <article class="bd-article">
 
-  <section id="unravel-voxel-stats-other-if-outliers-module">
-<span id="unravel-voxel-stats-other-if-outliers"></span><h1>unravel.voxel_stats.other.IF_outliers module<a class="headerlink" href="#unravel-voxel-stats-other-if-outliers-module" title="Link to this heading">#</a></h1>
+  <section id="module-unravel.voxel_stats.other.IF_outliers">
+<span id="unravel-voxel-stats-other-if-outliers-module"></span><span id="unravel-voxel-stats-other-if-outliers"></span><h1>unravel.voxel_stats.other.IF_outliers module<a class="headerlink" href="#module-unravel.voxel_stats.other.IF_outliers" title="Link to this heading">#</a></h1>
+<p>Loads .nii.gz images matching pattern, gets the mean intensity of voxels using the mask, checks for outliers (&gt;3*SD +/- the mean), and plots results</p>
+<section id="usage">
+<h2>Usage:<a class="headerlink" href="#usage" title="Link to this heading">#</a></h2>
+<blockquote>
+<div><p>path/IF_outliers.py -p ‘&lt;asterisk&gt;.nii.gz’ -m path/mask.nii.gz -o means_in_mask_plot.pdf -v</p>
+</div></blockquote>
+</section>
+<dl class="py function">
+<dt class="sig sig-object py" id="unravel.voxel_stats.other.IF_outliers.parse_args">
+<span class="sig-prename descclassname"><span class="pre">unravel.voxel_stats.other.IF_outliers.</span></span><span class="sig-name descname"><span class="pre">parse_args</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/unravel/voxel_stats/other/IF_outliers.html#parse_args"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#unravel.voxel_stats.other.IF_outliers.parse_args" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="unravel.voxel_stats.other.IF_outliers.mean_intensity_within_mask">
+<span class="sig-prename descclassname"><span class="pre">unravel.voxel_stats.other.IF_outliers.</span></span><span class="sig-name descname"><span class="pre">mean_intensity_within_mask</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">image</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/unravel/voxel_stats/other/IF_outliers.html#mean_intensity_within_mask"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#unravel.voxel_stats.other.IF_outliers.mean_intensity_within_mask" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="unravel.voxel_stats.other.IF_outliers.detect_outliers">
+<span class="sig-prename descclassname"><span class="pre">unravel.voxel_stats.other.IF_outliers.</span></span><span class="sig-name descname"><span class="pre">detect_outliers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">values</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/unravel/voxel_stats/other/IF_outliers.html#detect_outliers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#unravel.voxel_stats.other.IF_outliers.detect_outliers" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="unravel.voxel_stats.other.IF_outliers.main">
+<span class="sig-prename descclassname"><span class="pre">unravel.voxel_stats.other.IF_outliers.</span></span><span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/unravel/voxel_stats/other/IF_outliers.html#main"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#unravel.voxel_stats.other.IF_outliers.main" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
 </section>
 
 
@@ -533,6 +560,22 @@
                 <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
 
 
+  <div class="sidebar-secondary-item">
+<div
+    id="pst-page-navigation-heading-2"
+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
+  </div>
+  <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="#unravel.voxel_stats.other.IF_outliers.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.other.IF_outliers.mean_intensity_within_mask"><code class="docutils literal notranslate"><span class="pre">mean_intensity_within_mask()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.voxel_stats.other.IF_outliers.detect_outliers"><code class="docutils literal notranslate"><span class="pre">detect_outliers()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.voxel_stats.other.IF_outliers.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
+</ul>
+  </nav></div>
+
   <div class="sidebar-secondary-item">
 
   <div class="tocsection sourcelink">