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<section id="module-wonambi.attr.anat">
<span id="wonambi-attr-anat-module"></span><h1>wonambi.attr.anat module<a class="headerlink" href="#module-wonambi.attr.anat" title="Permalink to this heading"></a></h1>
<p>Module to read and return anatomical information, such as:
- surfaces, with class Surf
- brains, with class BrainSurf (both hemispheres)</p>
<dl class="py class">
<dt class="sig sig-object py" id="wonambi.attr.anat.Brain">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">wonambi.attr.anat.</span></span><span class="sig-name descname"><span class="pre">Brain</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">freesurfer_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surf_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pial'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Brain"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Brain" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Class that contains the left and right hemispheres.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>freesurfer_dir</strong> (<em>str</em>) – subject-specific directory created by freesurfer</p></li>
<li><p><strong>surf_type</strong> (<em>str</em>) – ‘pial’, ‘smoothwm’, ‘inflated’, ‘white’, or ‘sphere’</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="wonambi.attr.anat.Freesurfer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">wonambi.attr.anat.</span></span><span class="sig-name descname"><span class="pre">Freesurfer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">freesurfer_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fs_lut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Freesurfer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Freesurfer" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Provide class Freesurfer, with the information from freesurfer.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>freesurfer_dir</strong> (<em>str</em><em> or </em><a class="reference internal" href="wonambi.widgets.utils.html#wonambi.widgets.utils.Path" title="wonambi.widgets.utils.Path"><em>Path</em></a>) – subject-specific directory created by freesurfer</p></li>
<li><p><strong>fs_lut</strong> (<em>str</em><em> or </em><a class="reference internal" href="wonambi.widgets.utils.html#wonambi.widgets.utils.Path" title="wonambi.widgets.utils.Path"><em>Path</em></a>) – path to file called FreeSurferColorLUT.txt</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>It’s necessary that Freesurfer is installed and that the environmental
variable ‘FREESURFER_HOME’ is present.</p>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.attr.anat.Freesurfer.find_brain_region">
<span class="sig-name descname"><span class="pre">find_brain_region</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">abs_pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parc_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'aparc'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_approx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_regions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Freesurfer.find_brain_region"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Freesurfer.find_brain_region" title="Permalink to this definition"></a></dt>
<dd><p>Find the name of the brain region in which an electrode is located.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>abs_pos</strong> (<em>numpy.ndarray</em>) – 3x0 vector with the position of interest.</p></li>
<li><p><strong>parc_type</strong> (<em>str</em>) – ‘aparc’, ‘aparc.a2009s’, ‘BA’, ‘BA.thresh’, or ‘aparc.DKTatlas40’
‘aparc.DKTatlas40’ is only for recent freesurfer versions</p></li>
<li><p><strong>max_approx</strong> (<em>int</em><em>, </em><em>optional</em>) – max approximation to define position of the electrode.</p></li>
<li><p><strong>exclude_regions</strong> (<em>list</em><em> of </em><em>str</em><em> or </em><em>empty list</em>) – do not report regions if they contain these substrings. None means
that it does not exclude any region.</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>It determines the possible brain region in which one electrode is
present, based on Freesurfer segmentation. You can imagine that
sometimes one electrode is not perfectly located within one region,
but it’s a few mm away. The parameter “approx” specifies this tolerance
where each value is one mm. It keeps on searching in larger and larger
spots until it finds at least one region which is not white matter. If
there are multiple regions, it returns the region with the most
detection.
Minimal value is 0, which means only if the electrode is in the
precise location.</p>
<dl class="simple">
<dt>If you want to exclude white matter regions with ‘aparc’, use</dt><dd><p>exclude_regions = (‘White’, ‘WM’, ‘Unknown’)</p>
</dd>
<dt>and with ‘aparc.a2009s’, use:</dt><dd><p>exclude_regions = (‘White-Matter’)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.attr.anat.Freesurfer.read_brain">
<span class="sig-name descname"><span class="pre">read_brain</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">surf_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pial'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Freesurfer.read_brain"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Freesurfer.read_brain" title="Permalink to this definition"></a></dt>
<dd><p>Read the surface of both hemispheres.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>surf_type</strong> (<em>str</em>) – ‘pial’, ‘smoothwm’, ‘inflated’, ‘white’, or ‘sphere’</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><em>instance of Brain</em> – the surfaces of both brain hemispheres</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.attr.anat.Freesurfer.read_label">
<span class="sig-name descname"><span class="pre">read_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hemi</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parc_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'aparc'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Freesurfer.read_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Freesurfer.read_label" title="Permalink to this definition"></a></dt>
<dd><p>Read the labels (annotations) for each hemisphere.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>hemi</strong> (<em>str</em>) – ‘lh’ or ‘rh’</p></li>
<li><p><strong>parc_type</strong> (<em>str</em>) – ‘aparc’, ‘aparc.a2009s’, ‘BA’, ‘BA.thresh’, or ‘aparc.DKTatlas40’
‘aparc.DKTatlas40’ is only for recent freesurfer versions</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p><em>numpy.ndarray</em> – value at each vertex, indicating the label</p></li>
<li><p><em>numpy.ndarray</em> – RGB + alpha colors for each label</p></li>
<li><p><em>list of str</em> – names of the labels</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.attr.anat.Freesurfer.read_seg">
<span class="sig-name descname"><span class="pre">read_seg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parc_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'aparc'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Freesurfer.read_seg"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Freesurfer.read_seg" title="Permalink to this definition"></a></dt>
<dd><p>Read the MRI segmentation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>parc_type</strong> (<em>str</em>) – ‘aparc’ or ‘aparc.a2009s’</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p><em>numpy.ndarray</em> – 3d matrix with values</p></li>
<li><p><em>numpy.ndarray</em> – 4x4 affine matrix</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="wonambi.attr.anat.Freesurfer.surface_ras_shift">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">surface_ras_shift</span></span><a class="headerlink" href="#wonambi.attr.anat.Freesurfer.surface_ras_shift" title="Permalink to this definition"></a></dt>
<dd><p>one for volumes (“RAS”) and
one for surfaces (“tkReg”, “tkRAS”, and “Surface RAS”).
To get from surface to volume coordinates, add this numbers.
To get from volume to surface coordinates, substract this numbers.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Freesurfer uses two coordinate systems</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="wonambi.attr.anat.Surf">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">wonambi.attr.anat.</span></span><span class="sig-name descname"><span class="pre">Surf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">surf_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#Surf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.Surf" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Provide class Surf, with the positions and connections of vertices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>surf_file</strong> (<em>str</em><em> or </em><a class="reference internal" href="wonambi.widgets.utils.html#wonambi.widgets.utils.Path" title="wonambi.widgets.utils.Path"><em>Path</em></a>) – freesurfer file containing the surface</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="wonambi.attr.anat.Surf.surf_file">
<span class="sig-name descname"><span class="pre">surf_file</span></span><a class="headerlink" href="#wonambi.attr.anat.Surf.surf_file" title="Permalink to this definition"></a></dt>
<dd><p>freesurfer file containing the surface</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>path to file</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="wonambi.attr.anat.Surf.vert">
<span class="sig-name descname"><span class="pre">vert</span></span><a class="headerlink" href="#wonambi.attr.anat.Surf.vert" title="Permalink to this definition"></a></dt>
<dd><p>vertices of the mesh</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="wonambi.attr.anat.Surf.tri">
<span class="sig-name descname"><span class="pre">tri</span></span><a class="headerlink" href="#wonambi.attr.anat.Surf.tri" title="Permalink to this definition"></a></dt>
<dd><p>triangulation of the mesh</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.attr.anat.import_freesurfer_LUT">
<span class="sig-prename descclassname"><span class="pre">wonambi.attr.anat.</span></span><span class="sig-name descname"><span class="pre">import_freesurfer_LUT</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fs_lut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/attr/anat.html#import_freesurfer_LUT"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.attr.anat.import_freesurfer_LUT" title="Permalink to this definition"></a></dt>
<dd><p>Import Look-up Table with colors and labels for anatomical regions.</p>
<p>It’s necessary that Freesurfer is installed and that the environmental
variable ‘FREESURFER_HOME’ is present.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>fs_lut</strong> (<em>str</em><em> or </em><a class="reference internal" href="wonambi.widgets.utils.html#wonambi.widgets.utils.Path" title="wonambi.widgets.utils.Path"><em>Path</em></a>) – path to file called FreeSurferColorLUT.txt</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>idx</strong> (<em>list of int</em>) – indices of regions</p></li>
<li><p><strong>label</strong> (<em>list of str</em>) – names of the brain regions</p></li>
<li><p><strong>rgba</strong> (<em>numpy.ndarray</em>) – one row is a brain region and the columns are the RGB + alpha colors</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>
</section>
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