make html

unravel/docs/_build/html/_modules/unravel/region_stats/rstats.html

@@ -363,7 +363,7 @@ <h1>Source code for unravel.region_stats.rstats</h1><div class="highlight"><pre>
 <span class="sd">    rstats -s rel_path/segmentation_image.nii.gz -m path/atlas_split.nii.gz -c Saline --dirs sample14 sample36</span>
 
 <span class="sd">Outputs:</span>
-<span class="sd">    - CSV file with cell counts, region volumes, or cell densities for each region</span>
+<span class="sd">    - CSV files in ./sample??/regional_stats/ with cell counts, region volumes, or cell densities for each region</span>
 
 <span class="sd">Notes </span>
 <span class="sd">    - Regarding --type, also use &#39;counts&#39; or &#39;cell_desities&#39; for object counts or object densities</span>
@@ -403,7 +403,7 @@ <h1>Source code for unravel.region_stats.rstats</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;-t&#39;</span><span class="p">,</span> <span class="s1">&#39;--type&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Type of measurement (options: counts, volumes, cell_densities [default])&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;cell_densities&#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;-c&#39;</span><span class="p">,</span> <span class="s1">&#39;--condition&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;One word name for group (prepended to sample ID for rstats_summary)&#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;-s&#39;</span><span class="p">,</span> <span class="s1">&#39;--seg_img_path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;rel_path/segmentation_image.nii.gz (can be glob pattern)&#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;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas_path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;rel_path/native_atlas_split.nii.gz (only use this option if this file exists; left label IDs increased by 20,000)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</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_path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;rel_path/native_atlas_split.nii.gz (use this -a if this exists from ``warp_to_native``, otherwise use -m ; &quot;split&quot; == left label IDs increased by 20,000)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</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;-m&#39;</span><span class="p">,</span> <span class="s1">&#39;--moving_img&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas_image.nii.gz to warp from atlas space&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</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;-md&#39;</span><span class="p">,</span> <span class="s1">&#39;--metadata&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/metadata.txt. Default: ./parameters/metadata.txt&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;./parameters/metadata.txt&quot;</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;-cc&#39;</span><span class="p">,</span> <span class="s1">&#39;--connect&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Connected component connectivity (6, 18, or 26). Default: 6&#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">6</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>

unravel/docs/_build/html/_modules/unravel/register/reg_prep.html

@@ -403,7 +403,6 @@ <h1>Source code for unravel.register.reg_prep</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;-td&#39;</span><span class="p">,</span> <span class="s1">&#39;--target_dir&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/target_dir name to copy specific slices for seg_brain_mask (see usage)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</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;-s&#39;</span><span class="p">,</span> <span class="s1">&#39;--slices&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;List of slice numbers to copy, e.g., 0000 0400 0800&#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="nb">type</span><span class="o">=</span><span class="nb">str</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;-mi&#39;</span><span class="p">,</span> <span class="s1">&#39;--miracl&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Include reorientation step to mimic MIRACL&#39;s tif to .nii.gz conversion&quot;</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">default</span><span class="o">=</span><span class="kc">False</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">action</span><span class="o">=</span><span class="s1">&#39;store_true&#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">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. Default: False&#39;</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">default</span><span class="o">=</span><span class="kc">False</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>

unravel/docs/_build/html/unravel/region_stats/rstats.html

@@ -504,7 +504,7 @@ <h2>Usage if the native atlas is not available; it is not saved (faster):<a clas
 </div></blockquote>
 <dl class="simple">
 <dt>Outputs:</dt><dd><ul class="simple">
-<li><p>CSV file with cell counts, region volumes, or cell densities for each region</p></li>
+<li><p>CSV files in ./sample??/regional_stats/ with cell counts, region volumes, or cell densities for each region</p></li>
 </ul>
 </dd>
 <dt>Notes</dt><dd><ul class="simple">