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<section id="input-output-module">
<h1>Input/output module<a class="headerlink" href="#input-output-module" title="Link to this heading"></a></h1>
<section id="converting-dicom-to-bids-with-dcm2bids">
<h2>Converting DICOM to BIDS with dcm2bids<a class="headerlink" href="#converting-dicom-to-bids-with-dcm2bids" title="Link to this heading"></a></h2>
<p>Note that the DCM2BIDS documentation has details on how to install and use dcm2bids. Here, I only recorded how I did it.</p>
<section id="install-dcm2bids">
<h3>Install dcm2bids<a class="headerlink" href="#install-dcm2bids" title="Link to this heading"></a></h3>
<p>Full installation instructions can be found <a class="reference external" href="https://unfmontreal.github.io/Dcm2Bids/3.0.1/get-started/install/">here</a>.</p>
<ul class="simple">
<li><p>Create a yml file with all prerequisites: <code class="docutils literal notranslate"><span class="pre">nano</span> <span class="pre">environment.yml</span></code></p></li>
<li><p>Copy paste the following to <em>environment.yml</em>.</p></li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">name</span><span class="p">:</span> <span class="n">dcm2bids</span>
<span class="n">channels</span><span class="p">:</span>
<span class="o">-</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span>
<span class="n">dependencies</span><span class="p">:</span>
<span class="o">-</span> <span class="n">python</span><span class="o">>=</span><span class="mf">3.7</span>
<span class="o">-</span> <span class="n">dcm2niix</span>
<span class="o">-</span> <span class="n">dcm2bids</span>
</pre></div>
</div>
<ul class="simple">
<li><p>Create a conda environment with <em>environment.yml</em>: <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">env</span> <span class="pre">create</span> <span class="pre">--file</span> <span class="pre">environment.yml</span></code></p></li>
<li><p>Activate environment: <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">activate</span> <span class="pre">dcm2bids</span></code></p></li>
<li><p>Verify that dcm2bids works: <code class="docutils literal notranslate"><span class="pre">dcm2bids</span> <span class="pre">--help</span></code></p></li>
</ul>
</section>
<section id="tutorial-go-through">
<h3>Tutorial go-through<a class="headerlink" href="#tutorial-go-through" title="Link to this heading"></a></h3>
<p>Tutorial can be found <a class="reference external" href="https://unfmontreal.github.io/Dcm2Bids/3.0.1/tutorial/">here</a>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">activate</span> <span class="n">dcm2bids</span>
<span class="n">mkdir</span> <span class="n">dcm2bids</span><span class="o">-</span><span class="n">tutorial</span>
<span class="n">cd</span> <span class="n">dcm2bids</span><span class="o">-</span><span class="n">tutorial</span>
<span class="n">dcm2bids_scaffold</span> <span class="c1"># Help structure and organise data in an effient way</span>
<span class="c1"># by creating automatically a basic directory structure</span>
<span class="c1"># and the core files according to BIDS specification.</span>
<span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">neurolabusc</span><span class="o">/</span><span class="n">dcm_qa_nih</span><span class="o">/</span> <span class="n">sourcedata</span><span class="o">/</span><span class="n">dcm_qa_nih</span> <span class="c1"># download/clone example DICOM data to sourcedata folder</span>
<span class="n">dcm2bids_helper</span> <span class="o">-</span><span class="n">d</span> <span class="n">sourcedata</span><span class="o">/</span><span class="n">dcm_qa_nih</span><span class="o">/</span><span class="n">In</span> <span class="c1"># convert DICOM to NIFTI and save in temporary folder *tmp_dcm2bids*,</span>
<span class="c1"># for inspection and making filters for the config file.</span>
</pre></div>
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</section>
<section id="running-dcm2bids-in-vci-mas2">
<h3>Running dcm2bids in VCI/MAS2<a class="headerlink" href="#running-dcm2bids-in-vci-mas2" title="Link to this heading"></a></h3>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">activate</span> <span class="n">dcm2bids</span>
</pre></div>
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