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<h1 class="title toc-ignore">Batch processing script</h1>
<h4 class="date">Last updated: October 14, 2024</h4>
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<div class="sourceCode" id="cb1"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="co">% Example batch script for Philips MEGA-PRESS data with accompanying water references and structural images</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">% Remember to check GannetPreInitialise.m has the appropriate settings for your data</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>data_dir <span class="op">=</span> <span class="st">'/Users/username/Documents/my_project/data'</span><span class="op">;</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a>metab <span class="op">=</span> {<span class="st">'S01_GABA_68_act.sdat'</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> <span class="st">'S02_GABA_68_act.sdat'</span></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a> <span class="st">'S03_GABA_68_act.sdat'</span>}<span class="op">;</span></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>metab <span class="op">=</span> <span class="fu">fullfile</span>(data_dir<span class="op">,</span> metab)<span class="op">;</span> <span class="co">% It is good practice to include the full path of files</span></span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> </span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a>water <span class="op">=</span> {<span class="st">'S01_GABA_68_ref.sdat'</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a> <span class="st">'S02_GABA_68_ref.sdat'</span></span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> <span class="st">'S03_GABA_68_ref.sdat'</span>}<span class="op">;</span></span>
<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a>water <span class="op">=</span> <span class="fu">fullfile</span>(data_dir<span class="op">,</span> water)<span class="op">;</span></span>
<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a></span>
<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a>anat <span class="op">=</span> {<span class="st">'S01_T1_anat.nii'</span></span>
<span id="cb1-17"><a href="#cb1-17" tabindex="-1"></a> <span class="st">'S02_T1_anat.nii'</span></span>
<span id="cb1-18"><a href="#cb1-18" tabindex="-1"></a> <span class="st">'S03_T1_anat.nii'</span>}<span class="op">;</span></span>
<span id="cb1-19"><a href="#cb1-19" tabindex="-1"></a>anat <span class="op">=</span> <span class="fu">fullfile</span>(data_dir<span class="op">,</span> anat)<span class="op">;</span></span>
<span id="cb1-20"><a href="#cb1-20" tabindex="-1"></a></span>
<span id="cb1-21"><a href="#cb1-21" tabindex="-1"></a>MRS <span class="op">=</span> GannetLoad(metab<span class="op">,</span> water)<span class="op">;</span></span>
<span id="cb1-22"><a href="#cb1-22" tabindex="-1"></a>MRS <span class="op">=</span> GannetFit(MRS)<span class="op">;</span></span>
<span id="cb1-23"><a href="#cb1-23" tabindex="-1"></a>MRS <span class="op">=</span> GannetCoRegister(MRS<span class="op">,</span> anat)<span class="op">;</span></span>
<span id="cb1-24"><a href="#cb1-24" tabindex="-1"></a>MRS <span class="op">=</span> GannetSegment(MRS)<span class="op">;</span></span>
<span id="cb1-25"><a href="#cb1-25" tabindex="-1"></a>MRS <span class="op">=</span> GannetQuantify(MRS)<span class="op">;</span></span></code></pre></div>
<div id="rmd-source-code">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</div>
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