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TIGRLab · Sep 26, 2024 · 28d8d9b · 28d8d9b
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diff --git a/.doctrees/api/datman.config.doctree b/.doctrees/api/datman.config.doctree
diff --git a/.doctrees/api/datman.dashboard.doctree b/.doctrees/api/datman.dashboard.doctree
diff --git a/.doctrees/api/datman.exceptions.doctree b/.doctrees/api/datman.exceptions.doctree
diff --git a/.doctrees/api/datman.exporters.doctree b/.doctrees/api/datman.exporters.doctree
diff --git a/.doctrees/api/datman.fs_log_scraper.doctree b/.doctrees/api/datman.fs_log_scraper.doctree
diff --git a/.doctrees/api/datman.header_checks.doctree b/.doctrees/api/datman.header_checks.doctree
diff --git a/.doctrees/api/datman.metrics.doctree b/.doctrees/api/datman.metrics.doctree
diff --git a/.doctrees/api/datman.scan.doctree b/.doctrees/api/datman.scan.doctree
diff --git a/.doctrees/api/datman.scan_list.doctree b/.doctrees/api/datman.scan_list.doctree
diff --git a/.doctrees/api/datman.scanid.doctree b/.doctrees/api/datman.scanid.doctree
diff --git a/.doctrees/api/datman.utils.doctree b/.doctrees/api/datman.utils.doctree
diff --git a/.doctrees/api/datman.xnat.doctree b/.doctrees/api/datman.xnat.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/script_overview.doctree b/.doctrees/script_overview.doctree
diff --git a/_sources/script_overview.rst.txt b/_sources/script_overview.rst.txt
@@ -224,4 +224,22 @@ dm_parse_faces
 +----------------------------+----------------------------------------------+
 | **Additional Software**    |                                              |
 | **Dependencies**           | None                                         |
++----------------------------+----------------------------------------------+
+
+dm_update_standards
+*******************
++----------------------------+----------------------------------------------+
+| **Description**            | Update the gold standards for a study. The   |
+|                            | scans chosen as gold standards should have   |
+|                            | correct header values that all new scans can |
+|                            | be compared against.                         |
++----------------------------+----------------------------------------------+
+| **Environment Variables**  | None                                         |
++----------------------------+----------------------------------------------+
+| **Config Settings**        | * :ref:`Paths (std) <config Paths>`          |
++----------------------------+----------------------------------------------+
+| **Additional Config Files**| None                                         |
++----------------------------+----------------------------------------------+
+| **Additional Software**    |                                              |
+| **Dependencies**           | None                                         |
 +----------------------------+----------------------------------------------+
diff --git a/api/datman.config.html b/api/datman.config.html
diff --git a/api/datman.dashboard.html b/api/datman.dashboard.html
diff --git a/api/datman.exceptions.html b/api/datman.exceptions.html
@@ -107,64 +107,64 @@
 <p>Defines the exceptions used by datman sub-modules</p>
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.ConfigException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ConfigException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ConfigException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ConfigException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ConfigException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.DashboardException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">DashboardException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L25"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.DashboardException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">DashboardException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L25"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.DashboardException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 <p>Default exception for dashboard errors</p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.ExportException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ExportException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L40"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ExportException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ExportException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L40"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ExportException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.ExporterException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ExporterException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L31"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ExporterException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ExporterException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L31"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ExporterException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 <p>Default exception for errors exporting data from raw.</p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.InputException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">InputException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L44"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.InputException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">InputException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L44"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.InputException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.MetadataException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">MetadataException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L36"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.MetadataException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">MetadataException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L36"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.MetadataException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.ParseException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ParseException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L4"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ParseException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">ParseException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L4"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.ParseException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 <p>For participant ID parsing issues.</p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.QCException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">QCException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L56"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.QCException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">QCException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L56"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.QCException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.UndefinedSetting">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">UndefinedSetting</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L52"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.UndefinedSetting" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">UndefinedSetting</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L52"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.UndefinedSetting" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 </dd></dl>
 
 <dl class="py exception">
 <dt class="sig sig-object py" id="datman.exceptions.XnatException">
-<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">XnatException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/d1e7ed9/datman/exceptions.py#L10"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.XnatException" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">datman.exceptions.</span></span><span class="sig-name descname"><span class="pre">XnatException</span></span><a class="reference external" href="https://github.com/tigrlab/datman/blob/4c9c19e/datman/exceptions.py#L10"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#datman.exceptions.XnatException" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#Exception" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></a></p>
 <p>Default exception for XNAT errors</p>
 <dl class="py attribute">