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<h1 class="title toc-ignore">GannetPreInitialise settings</h1>
<h4 class="date">Last updated: October 14, 2024</h4>
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may be using a different release that has older/newer variables that
could result in an error during the analysis pipeline.</p>
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<div id="section"
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<h2 class="tabset tabset-fade tabset-pills"></h2>
<div id="gaba-edited-mega-press-data" class="section level3 hasAnchor">
<h3 class="hasAnchor">GABA-edited MEGA-PRESS data<a
href="#gaba-edited-mega-press-data" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<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">% Acquisition parameters</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> MRS_struct.p.target <span class="op">=</span> {<span class="st">'GABAGlx'</span>}<span class="op">;</span> <span class="co">% Edited metabolite(s) of interest; permitted options are:</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="co">% If MEGA-PRESS:</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> <span class="co">% {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> <span class="co">% If HERMES:</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a> <span class="co">% {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> <span class="co">% If HERCULES:</span></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a> <span class="co">% {'GABAGlx','GSH'}</span></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a> <span class="co">% If phantom data:</span></span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> <span class="co">% and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a> <span class="co">% and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a> MRS_struct.p.seqorig <span class="op">=</span> <span class="st">'JHU'</span><span class="op">;</span> <span class="co">% Origin of Philips MEGA-PRESS or GE HERMES sequences;</span></span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> <span class="co">% options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)</span></span>
<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a> </span>
<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a><span class="co">% Analysis parameters</span></span>
<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a> MRS_struct.p.LB <span class="op">=</span> <span class="fl">3</span><span class="op">;</span> <span class="co">% Exponential line-broadening (in Hz)</span></span>
<span id="cb1-17"><a href="#cb1-17" tabindex="-1"></a> MRS_struct.p.water_ECC <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, perform eddy current correction on water data</span></span>
<span id="cb1-18"><a href="#cb1-18" tabindex="-1"></a> MRS_struct.p.metab_ECC <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES, perform eddy current correction on metabolite data (requires a water reference)</span></span>
<span id="cb1-19"><a href="#cb1-19" tabindex="-1"></a> MRS_struct.p.water_removal <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, remove residual water signal in DIFF spectrum using HSVD</span></span>
<span id="cb1-20"><a href="#cb1-20" tabindex="-1"></a> MRS_struct.p.alignment <span class="op">=</span> <span class="st">'RobustSpecReg'</span><span class="op">;</span> <span class="co">% Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',</span></span>
<span id="cb1-21"><a href="#cb1-21" tabindex="-1"></a> <span class="co">% 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)</span></span>
<span id="cb1-22"><a href="#cb1-22" tabindex="-1"></a> MRS_struct.p.use_prealign_ref <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in</span></span>
<span id="cb1-23"><a href="#cb1-23" tabindex="-1"></a> <span class="co">% worse alignment compared to the pre-aligned data; setting this parameter to 1 will</span></span>
<span id="cb1-24"><a href="#cb1-24" tabindex="-1"></a> <span class="co">% make RobustSpecReg use the averaged pre-aligned subspectra as references to align the</span></span>
<span id="cb1-25"><a href="#cb1-25" tabindex="-1"></a> <span class="co">% averaged post-aligned subspectra, which may improve the final alignment</span></span>
<span id="cb1-26"><a href="#cb1-26" tabindex="-1"></a> MRS_struct.p.vox <span class="op">=</span> {<span class="st">'vox1'</span>}<span class="op">;</span> <span class="co">% For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.</span></span>
<span id="cb1-27"><a href="#cb1-27" tabindex="-1"></a> MRS_struct.p.fit_resid_water <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor</span></span>
<span id="cb1-28"><a href="#cb1-28" tabindex="-1"></a> MRS_struct.p.weighted_averaging <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, average subspectra using weighted averaging</span></span>
<span id="cb1-29"><a href="#cb1-29" tabindex="-1"></a> </span>
<span id="cb1-30"><a href="#cb1-30" tabindex="-1"></a><span class="co">% Flags(0 = NO; 1 = YES)</span></span>
<span id="cb1-31"><a href="#cb1-31" tabindex="-1"></a> MRS_struct.p.HERMES <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using HERMES</span></span>
<span id="cb1-32"><a href="#cb1-32" tabindex="-1"></a> MRS_struct.p.HERCULES <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well</span></span>
<span id="cb1-33"><a href="#cb1-33" tabindex="-1"></a> MRS_struct.p.PRIAM <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using PRIAM</span></span>
<span id="cb1-34"><a href="#cb1-34" tabindex="-1"></a> MRS_struct.p.phantom <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data are from a phantom (assumes phantom was scanned at room temperature)</span></span>
<span id="cb1-35"><a href="#cb1-35" tabindex="-1"></a> MRS_struct.p.join <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Join multiple files (this can be batched across subjects)</span></span>
<span id="cb1-36"><a href="#cb1-36" tabindex="-1"></a> MRS_struct.p.mat <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Save MRS_struct as a .mat file</span></span>
<span id="cb1-37"><a href="#cb1-37" tabindex="-1"></a> MRS_struct.p.csv <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,</span></span>
<span id="cb1-38"><a href="#cb1-38" tabindex="-1"></a> <span class="co">% GannetSegment and GannetQuantify)</span></span>
<span id="cb1-39"><a href="#cb1-39" tabindex="-1"></a> MRS_struct.p.append <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet</span></span>
<span id="cb1-40"><a href="#cb1-40" tabindex="-1"></a> <span class="co">% folder to be added to the search path and Ghostscript to be installed)</span></span>
<span id="cb1-41"><a href="#cb1-41" tabindex="-1"></a> MRS_struct.p.hide <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Do not display output figures</span></span></code></pre></div>
</div>
<div id="gaba-gsh-edited-hermes-data" class="section level3 hasAnchor">
<h3 class="hasAnchor">GABA-/GSH-edited HERMES data<a
href="#gaba-gsh-edited-hermes-data" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb2"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co">% Acquisition parameters</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a> MRS_struct.p.target <span class="op">=</span> {<span class="st">'GABAGlx'</span><span class="op">,</span><span class="st">'GSH'</span>}<span class="op">;</span> <span class="co">% Edited metabolite(s) of interest; permitted options are:</span></span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a> <span class="co">% If MEGA-PRESS:</span></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a> <span class="co">% {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}</span></span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a> <span class="co">% If HERMES:</span></span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a> <span class="co">% {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}</span></span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a> <span class="co">% If HERCULES:</span></span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a> <span class="co">% {'GABAGlx','GSH'}</span></span>
<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a> <span class="co">% If phantom data:</span></span>
<span id="cb2-10"><a href="#cb2-10" tabindex="-1"></a> <span class="co">% and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}</span></span>
<span id="cb2-11"><a href="#cb2-11" tabindex="-1"></a> <span class="co">% and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}</span></span>
<span id="cb2-12"><a href="#cb2-12" tabindex="-1"></a> MRS_struct.p.seqorig <span class="op">=</span> <span class="st">'JHU'</span><span class="op">;</span> <span class="co">% Origin of Philips MEGA-PRESS or GE HERMES sequences;</span></span>
<span id="cb2-13"><a href="#cb2-13" tabindex="-1"></a> <span class="co">% options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)</span></span>
<span id="cb2-14"><a href="#cb2-14" tabindex="-1"></a> </span>
<span id="cb2-15"><a href="#cb2-15" tabindex="-1"></a><span class="co">% Analysis parameters</span></span>
<span id="cb2-16"><a href="#cb2-16" tabindex="-1"></a> MRS_struct.p.LB <span class="op">=</span> <span class="fl">3</span><span class="op">;</span> <span class="co">% Exponential line-broadening (in Hz)</span></span>
<span id="cb2-17"><a href="#cb2-17" tabindex="-1"></a> MRS_struct.p.water_ECC <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, perform eddy current correction on water data</span></span>
<span id="cb2-18"><a href="#cb2-18" tabindex="-1"></a> MRS_struct.p.metab_ECC <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES, perform eddy current correction on metabolite data (requires a water reference)</span></span>
<span id="cb2-19"><a href="#cb2-19" tabindex="-1"></a> MRS_struct.p.water_removal <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, remove residual water signal in DIFF spectrum using HSVD</span></span>
<span id="cb2-20"><a href="#cb2-20" tabindex="-1"></a> MRS_struct.p.alignment <span class="op">=</span> <span class="st">'RobustSpecReg'</span><span class="op">;</span> <span class="co">% Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',</span></span>
<span id="cb2-21"><a href="#cb2-21" tabindex="-1"></a> <span class="co">% 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)</span></span>
<span id="cb2-22"><a href="#cb2-22" tabindex="-1"></a> MRS_struct.p.use_prealign_ref <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in</span></span>
<span id="cb2-23"><a href="#cb2-23" tabindex="-1"></a> <span class="co">% worse alignment compared to the pre-aligned data; setting this parameter to 1 will</span></span>
<span id="cb2-24"><a href="#cb2-24" tabindex="-1"></a> <span class="co">% make RobustSpecReg use the averaged pre-aligned subspectra as references to align the</span></span>
<span id="cb2-25"><a href="#cb2-25" tabindex="-1"></a> <span class="co">% averaged post-aligned subspectra, which may improve the final alignment</span></span>
<span id="cb2-26"><a href="#cb2-26" tabindex="-1"></a> MRS_struct.p.vox <span class="op">=</span> {<span class="st">'vox1'</span>}<span class="op">;</span> <span class="co">% For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.</span></span>
<span id="cb2-27"><a href="#cb2-27" tabindex="-1"></a> MRS_struct.p.fit_resid_water <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor</span></span>
<span id="cb2-28"><a href="#cb2-28" tabindex="-1"></a> MRS_struct.p.weighted_averaging <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, average subspectra using weighted averaging</span></span>
<span id="cb2-29"><a href="#cb2-29" tabindex="-1"></a> </span>
<span id="cb2-30"><a href="#cb2-30" tabindex="-1"></a><span class="co">% Flags(0 = NO; 1 = YES)</span></span>
<span id="cb2-31"><a href="#cb2-31" tabindex="-1"></a> MRS_struct.p.HERMES <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% Data acquired using HERMES</span></span>
<span id="cb2-32"><a href="#cb2-32" tabindex="-1"></a> MRS_struct.p.HERCULES <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well</span></span>
<span id="cb2-33"><a href="#cb2-33" tabindex="-1"></a> MRS_struct.p.PRIAM <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using PRIAM</span></span>
<span id="cb2-34"><a href="#cb2-34" tabindex="-1"></a> MRS_struct.p.phantom <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data are from a phantom (assumes phantom was scanned at room temperature)</span></span>
<span id="cb2-35"><a href="#cb2-35" tabindex="-1"></a> MRS_struct.p.join <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Join multiple files (this can be batched across subjects)</span></span>
<span id="cb2-36"><a href="#cb2-36" tabindex="-1"></a> MRS_struct.p.mat <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Save MRS_struct as a .mat file</span></span>
<span id="cb2-37"><a href="#cb2-37" tabindex="-1"></a> MRS_struct.p.csv <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,</span></span>
<span id="cb2-38"><a href="#cb2-38" tabindex="-1"></a> <span class="co">% GannetSegment and GannetQuantify)</span></span>
<span id="cb2-39"><a href="#cb2-39" tabindex="-1"></a> MRS_struct.p.append <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet</span></span>
<span id="cb2-40"><a href="#cb2-40" tabindex="-1"></a> <span class="co">% folder to be added to the search path and Ghostscript to be installed)</span></span>
<span id="cb2-41"><a href="#cb2-41" tabindex="-1"></a> MRS_struct.p.hide <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Do not display output figures</span></span></code></pre></div>
</div>
<div id="phantom-gaba-edited-mega-press-data"
class="section level3 hasAnchor">
<h3 class="hasAnchor">Phantom GABA-edited MEGA-PRESS data<a
href="#phantom-gaba-edited-mega-press-data" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb3"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="co">% Acquisition parameters</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a> MRS_struct.p.target <span class="op">=</span> {<span class="st">'GABA'</span>}<span class="op">;</span> <span class="co">% Edited metabolite(s) of interest; permitted options are:</span></span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a> <span class="co">% If MEGA-PRESS:</span></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a> <span class="co">% {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}</span></span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a> <span class="co">% If HERMES:</span></span>
<span id="cb3-6"><a href="#cb3-6" tabindex="-1"></a> <span class="co">% {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}</span></span>
<span id="cb3-7"><a href="#cb3-7" tabindex="-1"></a> <span class="co">% If HERCULES:</span></span>
<span id="cb3-8"><a href="#cb3-8" tabindex="-1"></a> <span class="co">% {'GABAGlx','GSH'}</span></span>
<span id="cb3-9"><a href="#cb3-9" tabindex="-1"></a> <span class="co">% If phantom data:</span></span>
<span id="cb3-10"><a href="#cb3-10" tabindex="-1"></a> <span class="co">% and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}</span></span>
<span id="cb3-11"><a href="#cb3-11" tabindex="-1"></a> <span class="co">% and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}</span></span>
<span id="cb3-12"><a href="#cb3-12" tabindex="-1"></a> MRS_struct.p.seqorig <span class="op">=</span> <span class="st">'JHU'</span><span class="op">;</span> <span class="co">% Origin of Philips MEGA-PRESS or GE HERMES sequences;</span></span>
<span id="cb3-13"><a href="#cb3-13" tabindex="-1"></a> <span class="co">% options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)</span></span>
<span id="cb3-14"><a href="#cb3-14" tabindex="-1"></a> </span>
<span id="cb3-15"><a href="#cb3-15" tabindex="-1"></a><span class="co">% Analysis parameters</span></span>
<span id="cb3-16"><a href="#cb3-16" tabindex="-1"></a> MRS_struct.p.LB <span class="op">=</span> <span class="fl">3</span><span class="op">;</span> <span class="co">% Exponential line-broadening (in Hz)</span></span>
<span id="cb3-17"><a href="#cb3-17" tabindex="-1"></a> MRS_struct.p.water_ECC <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, perform eddy current correction on water data</span></span>
<span id="cb3-18"><a href="#cb3-18" tabindex="-1"></a> MRS_struct.p.metab_ECC <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES, perform eddy current correction on metabolite data (requires a water reference)</span></span>
<span id="cb3-19"><a href="#cb3-19" tabindex="-1"></a> MRS_struct.p.water_removal <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, remove residual water signal in DIFF spectrum using HSVD</span></span>
<span id="cb3-20"><a href="#cb3-20" tabindex="-1"></a> MRS_struct.p.alignment <span class="op">=</span> <span class="st">'none'</span><span class="op">;</span> <span class="co">% Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',</span></span>
<span id="cb3-21"><a href="#cb3-21" tabindex="-1"></a> <span class="co">% 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)</span></span>
<span id="cb3-22"><a href="#cb3-22" tabindex="-1"></a> MRS_struct.p.use_prealign_ref <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in</span></span>
<span id="cb3-23"><a href="#cb3-23" tabindex="-1"></a> <span class="co">% worse alignment compared to the pre-aligned data; setting this parameter to 1 will</span></span>
<span id="cb3-24"><a href="#cb3-24" tabindex="-1"></a> <span class="co">% make RobustSpecReg use the averaged pre-aligned subspectra as references to align the</span></span>
<span id="cb3-25"><a href="#cb3-25" tabindex="-1"></a> <span class="co">% averaged post-aligned subspectra, which may improve the final alignment</span></span>
<span id="cb3-26"><a href="#cb3-26" tabindex="-1"></a> MRS_struct.p.vox <span class="op">=</span> {<span class="st">'vox1'</span>}<span class="op">;</span> <span class="co">% For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.</span></span>
<span id="cb3-27"><a href="#cb3-27" tabindex="-1"></a> MRS_struct.p.fit_resid_water <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor</span></span>
<span id="cb3-28"><a href="#cb3-28" tabindex="-1"></a> MRS_struct.p.weighted_averaging <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% 1 = YES, average subspectra using weighted averaging</span></span>
<span id="cb3-29"><a href="#cb3-29" tabindex="-1"></a> </span>
<span id="cb3-30"><a href="#cb3-30" tabindex="-1"></a><span class="co">% Flags(0 = NO; 1 = YES)</span></span>
<span id="cb3-31"><a href="#cb3-31" tabindex="-1"></a> MRS_struct.p.HERMES <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using HERMES</span></span>
<span id="cb3-32"><a href="#cb3-32" tabindex="-1"></a> MRS_struct.p.HERCULES <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well</span></span>
<span id="cb3-33"><a href="#cb3-33" tabindex="-1"></a> MRS_struct.p.PRIAM <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Data acquired using PRIAM</span></span>
<span id="cb3-34"><a href="#cb3-34" tabindex="-1"></a> MRS_struct.p.phantom <span class="op">=</span> <span class="fl">1</span><span class="op">;</span> <span class="co">% Data are from a phantom (assumes phantom was scanned at room temperature)</span></span>
<span id="cb3-35"><a href="#cb3-35" tabindex="-1"></a> MRS_struct.p.join <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Join multiple files (this can be batched across subjects)</span></span>
<span id="cb3-36"><a href="#cb3-36" tabindex="-1"></a> MRS_struct.p.mat <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Save MRS_struct as a .mat file</span></span>
<span id="cb3-37"><a href="#cb3-37" tabindex="-1"></a> MRS_struct.p.csv <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,</span></span>
<span id="cb3-38"><a href="#cb3-38" tabindex="-1"></a> <span class="co">% GannetSegment and GannetQuantify)</span></span>
<span id="cb3-39"><a href="#cb3-39" tabindex="-1"></a> MRS_struct.p.append <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet</span></span>
<span id="cb3-40"><a href="#cb3-40" tabindex="-1"></a> <span class="co">% directory to be added to the search path and Ghostscript to be installed)</span></span>
<span id="cb3-41"><a href="#cb3-41" tabindex="-1"></a> MRS_struct.p.hide <span class="op">=</span> <span class="fl">0</span><span class="op">;</span> <span class="co">% Do not display output figures</span></span></code></pre></div>
</div>
</div>
<div id="rmd-source-code">---
title: "GannetPreInitialise settings"
date: "Last updated: `r format(Sys.time(), '%B %d, %Y')`"
output: html_document
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r, child = "js/back-to-top.js"}
```

```{css, echo = FALSE}
body .main-container {
  max-width: 1200px;
}
```

<br>

::: warning
<i class="fa fa-exclamation-circle" style="color: white"></i>&nbsp; These examples were created in release 3.3.0. Take care copy-pasting these examples into your version of `GannetPreInitialise.m`. You may be using a different release that has older/newer variables that could result in an error during the analysis pipeline.
:::

## {.tabset .tabset-fade .tabset-pills}

### GABA-edited MEGA-PRESS data

```{octave, eval = FALSE}
% Acquisition parameters
    MRS_struct.p.target = {'GABAGlx'}; % Edited metabolite(s) of interest; permitted options are:
                                       % If MEGA-PRESS:
                                       %   {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                       % If HERMES:
                                       %   {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
                                       % If HERCULES:
                                       %   {'GABAGlx','GSH'}
                                       % If phantom data:
                                       %   and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                       %   and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
    MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
                                  % options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
    
% Analysis parameters
    MRS_struct.p.LB            = 3; % Exponential line-broadening (in Hz)
    MRS_struct.p.water_ECC     = 1; % 1 = YES, perform eddy current correction on water data
    MRS_struct.p.metab_ECC     = 0; % 1 = YES, perform eddy current correction on metabolite data (requires a water reference)
    MRS_struct.p.water_removal = 1; % 1 = YES, remove residual water signal in DIFF spectrum using HSVD
    MRS_struct.p.alignment     = 'RobustSpecReg'; % Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',
                                                  % 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)
    MRS_struct.p.use_prealign_ref = 0; % 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in
                                       % worse alignment compared to the pre-aligned data; setting this parameter to 1 will
                                       % make RobustSpecReg use the averaged pre-aligned subspectra as references to align the
                                       % averaged post-aligned subspectra, which may improve the final alignment
    MRS_struct.p.vox                = {'vox1'}; % For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.
    MRS_struct.p.fit_resid_water    = 0; % 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor
    MRS_struct.p.weighted_averaging = 1; % 1 = YES, average subspectra using weighted averaging
    
% Flags(0 = NO; 1 = YES)
    MRS_struct.p.HERMES   = 0; % Data acquired using HERMES
    MRS_struct.p.HERCULES = 0; % Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well
    MRS_struct.p.PRIAM    = 0; % Data acquired using PRIAM
    MRS_struct.p.phantom  = 0; % Data are from a phantom (assumes phantom was scanned at room temperature)
    MRS_struct.p.join     = 0; % Join multiple files (this can be batched across subjects)
    MRS_struct.p.mat      = 0; % Save MRS_struct as a .mat file
    MRS_struct.p.csv      = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
                               % GannetSegment and GannetQuantify)
    MRS_struct.p.append   = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
                               % folder to be added to the search path and Ghostscript to be installed)
    MRS_struct.p.hide     = 0; % Do not display output figures
```

### GABA-/GSH-edited HERMES data

```{octave, eval = FALSE}
% Acquisition parameters
    MRS_struct.p.target = {'GABAGlx','GSH'}; % Edited metabolite(s) of interest; permitted options are:
                                       % If MEGA-PRESS:
                                       %   {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                       % If HERMES:
                                       %   {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
                                       % If HERCULES:
                                       %   {'GABAGlx','GSH'}
                                       % If phantom data:
                                       %   and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                       %   and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
    MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
                                  % options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
    
% Analysis parameters
    MRS_struct.p.LB            = 3; % Exponential line-broadening (in Hz)
    MRS_struct.p.water_ECC     = 1; % 1 = YES, perform eddy current correction on water data
    MRS_struct.p.metab_ECC     = 0; % 1 = YES, perform eddy current correction on metabolite data (requires a water reference)
    MRS_struct.p.water_removal = 1; % 1 = YES, remove residual water signal in DIFF spectrum using HSVD
    MRS_struct.p.alignment     = 'RobustSpecReg'; % Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',
                                                  % 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)
    MRS_struct.p.use_prealign_ref = 0; % 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in
                                       % worse alignment compared to the pre-aligned data; setting this parameter to 1 will
                                       % make RobustSpecReg use the averaged pre-aligned subspectra as references to align the
                                       % averaged post-aligned subspectra, which may improve the final alignment
    MRS_struct.p.vox                = {'vox1'}; % For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.
    MRS_struct.p.fit_resid_water    = 0; % 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor
    MRS_struct.p.weighted_averaging = 1; % 1 = YES, average subspectra using weighted averaging
    
% Flags(0 = NO; 1 = YES)
    MRS_struct.p.HERMES   = 1; % Data acquired using HERMES
    MRS_struct.p.HERCULES = 0; % Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well
    MRS_struct.p.PRIAM    = 0; % Data acquired using PRIAM
    MRS_struct.p.phantom  = 0; % Data are from a phantom (assumes phantom was scanned at room temperature)
    MRS_struct.p.join     = 0; % Join multiple files (this can be batched across subjects)
    MRS_struct.p.mat      = 0; % Save MRS_struct as a .mat file
    MRS_struct.p.csv      = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
                               % GannetSegment and GannetQuantify)
    MRS_struct.p.append   = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
                               % folder to be added to the search path and Ghostscript to be installed)
    MRS_struct.p.hide     = 0; % Do not display output figures
```

### Phantom GABA-edited MEGA-PRESS data

```{octave, eval = FALSE}
% Acquisition parameters
    MRS_struct.p.target = {'GABA'}; % Edited metabolite(s) of interest; permitted options are:
                                       % If MEGA-PRESS:
                                       %   {'GABA'}, {'GABAGlx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                       % If HERMES:
                                       %   {'GABAGlx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
                                       % If HERCULES:
                                       %   {'GABAGlx','GSH'}
                                       % If phantom data:
                                       %   and MEGA-PRESS: {'GABA'}, {'Glx'}, {'GSH'}, {'Lac'}, or {'EtOH'}
                                       %   and HERMES: {'GABA','GSH'}, {'Glx','GSH'}, {'Lac','GSH'}, or {'EtOH','GABA','GSH'}
    MRS_struct.p.seqorig = 'JHU'; % Origin of Philips MEGA-PRESS or GE HERMES sequences;
                                  % options are 'JHU' or 'Philips' if Philips, or 'Lythgoe' if GE (HERMES only)
    
% Analysis parameters
    MRS_struct.p.LB            = 3; % Exponential line-broadening (in Hz)
    MRS_struct.p.water_ECC     = 1; % 1 = YES, perform eddy current correction on water data
    MRS_struct.p.metab_ECC     = 0; % 1 = YES, perform eddy current correction on metabolite data (requires a water reference)
    MRS_struct.p.water_removal = 1; % 1 = YES, remove residual water signal in DIFF spectrum using HSVD
    MRS_struct.p.alignment     = 'none'; % Alignment method; options are 'RobustSpecReg' (recommended), 'SpecReg', 'SpecRegHERMES',
                                                  % 'Cr', 'Cho', 'NAA', 'H2O', 'CrOFF', or 'none' (recommended for phantom data)
    MRS_struct.p.use_prealign_ref = 0; % 1 = YES; in some cases, using RobustSpecReg to align HERMES/HERCULES data can result in
                                       % worse alignment compared to the pre-aligned data; setting this parameter to 1 will
                                       % make RobustSpecReg use the averaged pre-aligned subspectra as references to align the
                                       % averaged post-aligned subspectra, which may improve the final alignment
    MRS_struct.p.vox                = {'vox1'}; % For naming voxels in PRIAM data, e.g. {'anterior','posterior'}, {'right','left'}, etc.
    MRS_struct.p.fit_resid_water    = 0; % 1 = YES, fit the residual water signal in the OFF spectrum to calculate a water suppression factor
    MRS_struct.p.weighted_averaging = 1; % 1 = YES, average subspectra using weighted averaging
    
% Flags(0 = NO; 1 = YES)
    MRS_struct.p.HERMES   = 0; % Data acquired using HERMES
    MRS_struct.p.HERCULES = 0; % Data acquired using HERCULES; if 1, MRS_struct.p.HERMES must be set to 1 as well
    MRS_struct.p.PRIAM    = 0; % Data acquired using PRIAM
    MRS_struct.p.phantom  = 1; % Data are from a phantom (assumes phantom was scanned at room temperature)
    MRS_struct.p.join     = 0; % Join multiple files (this can be batched across subjects)
    MRS_struct.p.mat      = 0; % Save MRS_struct as a .mat file
    MRS_struct.p.csv      = 0; % Extract useful data from MRS_struct and export them to a .csv file (applies to GannetFit,
                               % GannetSegment and GannetQuantify)
    MRS_struct.p.append   = 0; % Append PDF outputs into one PDF (separately for each module) (requires export_fig in the Gannet
                               % directory to be added to the search path and Ghostscript to be installed)
    MRS_struct.p.hide     = 0; % Do not display output figures
```



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