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<!DOCTYPE html>
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<title>4. nidata.diffusion package — nidata documentation</title>
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<li><a class="reference internal" href="#">4. nidata.diffusion package</a><ul>
<li><a class="reference internal" href="#module-nidata.diffusion">4.1. Module contents</a></li>
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<div class="section" id="nidata-diffusion-package">
<h1>4. nidata.diffusion package<a class="headerlink" href="#nidata-diffusion-package" title="Permalink to this headline">¶</a></h1>
<div class="section" id="module-nidata.diffusion">
<span id="module-contents"></span><h2>4.1. Module contents<a class="headerlink" href="#module-nidata.diffusion" title="Permalink to this headline">¶</a></h2>
<dl class="exception">
<dt id="nidata.diffusion.FetcherError">
<em class="property">exception </em><code class="descclassname">nidata.diffusion.</code><code class="descname">FetcherError</code><a class="reference internal" href="_modules/nidata/diffusion.html#FetcherError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.FetcherError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">exceptions.Exception</span></code></p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.check_md5">
<code class="descclassname">nidata.diffusion.</code><code class="descname">check_md5</code><span class="sig-paren">(</span><em>filename</em>, <em>stored_md5</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#check_md5"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.check_md5" title="Permalink to this definition">¶</a></dt>
<dd><p>Computes the md5 of filename and check if it matches with the supplied string md5</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_data">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_data</code><span class="sig-paren">(</span><em>files</em>, <em>folder</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Downloads files to folder and checks their md5 checksums</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><p class="first"><strong>files</strong> : dictionary</p>
<blockquote>
<div><p>For each file in <cite>files</cite> the value should be (url, md5). The file will
be downloaded from url if the file does not already exist or if the
file exists but the md5 checksum does not match.</p>
</div></blockquote>
<p><strong>folder</strong> : str</p>
<blockquote>
<div><p>The directory where to save the file, the directory will be created if
it does not already exist.</p>
</div></blockquote>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first"><strong>FetcherError</strong></p>
<blockquote class="last">
<div><p>Raises if the md5 checksum of the file does not match the expected
value. The downloaded file is not deleted when this error is raised.</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_isbi2013_2shell">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_isbi2013_2shell</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_isbi2013_2shell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_isbi2013_2shell" title="Permalink to this definition">¶</a></dt>
<dd><p>Download a 2-shell software phantom dataset</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_scil_b0">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_scil_b0</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_scil_b0"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_scil_b0" title="Permalink to this definition">¶</a></dt>
<dd><p>Download b=0 datasets from multiple MR systems (GE, Philips, Siemens) and
different magnetic fields (1.5T and 3T)</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_sherbrooke_3shell">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_sherbrooke_3shell</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_sherbrooke_3shell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_sherbrooke_3shell" title="Permalink to this definition">¶</a></dt>
<dd><p>Download a 3shell HARDI dataset with 192 gradient directions</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_stanford_hardi">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_stanford_hardi</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_stanford_hardi"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_stanford_hardi" title="Permalink to this definition">¶</a></dt>
<dd><p>Download a HARDI dataset with 160 gradient directions</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_stanford_labels">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_stanford_labels</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_stanford_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_stanford_labels" title="Permalink to this definition">¶</a></dt>
<dd><p>Download reduced freesurfer aparc image from stanford web site.</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_stanford_pve_maps">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_stanford_pve_maps</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_stanford_pve_maps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_stanford_pve_maps" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_stanford_t1">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_stanford_t1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_stanford_t1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_stanford_t1" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_syn_data">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_syn_data</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_syn_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_syn_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Download t1 and b0 volumes from the same session</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.fetch_taiwan_ntu_dsi">
<code class="descclassname">nidata.diffusion.</code><code class="descname">fetch_taiwan_ntu_dsi</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#fetch_taiwan_ntu_dsi"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.fetch_taiwan_ntu_dsi" title="Permalink to this definition">¶</a></dt>
<dd><p>Download a DSI dataset with 203 gradient directions</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_isbi2013_2shell">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_isbi2013_2shell</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_isbi2013_2shell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_isbi2013_2shell" title="Permalink to this definition">¶</a></dt>
<dd><p>Load ISBI 2013 2-shell synthetic dataset</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>img</strong> : obj,</p>
<blockquote>
<div><p>Nifti1Image</p>
</div></blockquote>
<p><strong>gtab</strong> : obj,</p>
<blockquote class="last">
<div><p>GradientTable</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_scil_b0">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_scil_b0</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_scil_b0"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_scil_b0" title="Permalink to this definition">¶</a></dt>
<dd><p>Load GE 3T b0 image form the scil b0 dataset.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>img</strong> : obj,</p>
<blockquote class="last">
<div><p>Nifti1Image</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_sherbrooke_3shell">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_sherbrooke_3shell</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_sherbrooke_3shell"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_sherbrooke_3shell" title="Permalink to this definition">¶</a></dt>
<dd><p>Load Sherbrooke 3-shell HARDI dataset</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>img</strong> : obj,</p>
<blockquote>
<div><p>Nifti1Image</p>
</div></blockquote>
<p><strong>gtab</strong> : obj,</p>
<blockquote class="last">
<div><p>GradientTable</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_siemens_scil_b0">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_siemens_scil_b0</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_siemens_scil_b0"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_siemens_scil_b0" title="Permalink to this definition">¶</a></dt>
<dd><p>Load Siemens 1.5T b0 image form the scil b0 dataset.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>img</strong> : obj,</p>
<blockquote class="last">
<div><p>Nifti1Image</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_stanford_hardi">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_stanford_hardi</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_stanford_hardi"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_stanford_hardi" title="Permalink to this definition">¶</a></dt>
<dd><p>Load Stanford HARDI dataset</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>img</strong> : obj,</p>
<blockquote>
<div><p>Nifti1Image</p>
</div></blockquote>
<p><strong>gtab</strong> : obj,</p>
<blockquote class="last">
<div><p>GradientTable</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_stanford_labels">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_stanford_labels</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_stanford_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_stanford_labels" title="Permalink to this definition">¶</a></dt>
<dd><p>Read stanford hardi data and label map</p>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_stanford_pve_maps">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_stanford_pve_maps</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_stanford_pve_maps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_stanford_pve_maps" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_stanford_t1">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_stanford_t1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_stanford_t1"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_stanford_t1" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_syn_data">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_syn_data</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_syn_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_syn_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Load t1 and b0 volumes from the same session</p>
<table class="docutils field-list" frame="void" rules="none">
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<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>t1</strong> : obj,</p>
<blockquote>
<div><p>Nifti1Image</p>
</div></blockquote>
<p><strong>b0</strong> : obj,</p>
<blockquote class="last">
<div><p>Nifti1Image</p>
</div></blockquote>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="nidata.diffusion.read_taiwan_ntu_dsi">
<code class="descclassname">nidata.diffusion.</code><code class="descname">read_taiwan_ntu_dsi</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/nidata/diffusion.html#read_taiwan_ntu_dsi"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#nidata.diffusion.read_taiwan_ntu_dsi" title="Permalink to this definition">¶</a></dt>
<dd><p>Load Taiwan NTU dataset</p>
<table class="docutils field-list" frame="void" rules="none">
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<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>img</strong> : obj,</p>
<blockquote>
<div><p>Nifti1Image</p>
</div></blockquote>
<p><strong>gtab</strong> : obj,</p>
<blockquote class="last">
<div><p>GradientTable</p>
</div></blockquote>
</td>
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</tbody>
</table>
</dd></dl>
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<h3><a href="index.html">Table Of Contents</a></h3>
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<li><a class="reference internal" href="#">4. nidata.diffusion package</a><ul>
<li><a class="reference internal" href="#module-nidata.diffusion">4.1. Module contents</a></li>
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