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<h1 class="title toc-ignore">FAQ</h1>
<h4 class="date">Last updated: October 14, 2024</h4>
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<p><br></p>
<div class="info">
<p><i class="fa fa-info-circle" style="color: white"></i> When
encountering an error or bug in Gannet, please first check you are using
the latest
<a href="https://github.com/markmikkelsen/Gannet" target="_blank"><u>version</u></a>.
It may be that your issue has already been addressed.</p>
<p>If your issue has not been addressed or is not found in this FAQ,
please report the issue to us on
<a href="https://github.com/markmikkelsen/Gannet/issues" target="_blank"><u>GitHub</u></a>
or the
<a href="https://forum.mrshub.org/c/mrs-software/gannet/9" target="_blank"><u>MRSHub
Forum</u></a>.</p>
</div>
<div id="general" class="section level2 hasAnchor">
<h2 class="hasAnchor">General<a href="#general" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<div id="can-gannet-process-non-edited-data"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>1. Can Gannet process non-edited
data?</strong><a href="#can-gannet-process-non-edited-data"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>No, Gannet is designed to process edited single-voxel data only.
However, the standalone tool <a
href="https://markmikkelsen.github.io/Gannet-docs/additional-tools.html#coregstandalone">CoRegStandAlone</a>
can be used with non-edited single-voxel data to co-register voxels to
structural images and segment the images to obtain voxel tissue
fractions.</p>
</div>
<div id="can-gannet-process-mrsi-data" class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>2. Can Gannet process MRSI
data?</strong><a href="#can-gannet-process-mrsi-data"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>No.</p>
</div>
<div id="can-gannet-process-gsh-edited-data"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>3. Can Gannet process GSH-edited
data?</strong><a href="#can-gannet-process-gsh-edited-data"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>Yes, Gannet can process GABA-, GSH-, Lac-, and EtOH-edited MEGA-PRESS
data, as well as GABA-/GSH-, Lac-/GSH-, and EtOH-/GABA-/GSH-edited
HERMES and HERCULES data. (Fitting of HERCULES phantom data is not
supported, however.) Simply set the appropriate <code>target</code>
option(s) in <code>GannetPreInitialise.m</code>.</p>
</div>
<div id="can-gannet-process-hermeshercules-data"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>4. Can Gannet process HERMES/HERCULES
data?</strong><a href="#can-gannet-process-hermeshercules-data"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p><code>GannetLoad.m</code> can load and preprocess HERMES and HERCULES
data, but only HERMES data can be modeled in <code>GannetFit.m</code>.
HERCULES data can be fully processed and fitted using the
<a href="https://github.com/schorschinho/osprey" target="_blank">Osprey</a>
software package.</p>
</div>
<div id="can-gannet-process-phantom-data"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>5. Can Gannet process phantom
data?</strong><a href="#can-gannet-process-phantom-data"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>Yes, Gannet can process and fit phantom edited data as described
above. Make sure to set <code>phantom</code> to <code>1</code> under
<code>Flags</code> in <code>GannetPreInitialise.m</code>. If you want to
fit your data, run <code>GannetFitPhantom(MRS_struct);</code> instead of
<code>GannetFit(MRS_struct);</code>. (Fitting of HERCULES phantom data
is not supported.)</p>
</div>
</div>
<div id="output" class="section level2 hasAnchor">
<h2 class="hasAnchor">Output<a href="#output" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<div id="why-is-my-spectrum-upside-down"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>1. Why is my spectrum upside
down?</strong><a href="#why-is-my-spectrum-upside-down"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p><img id="img_50" src="images/faq/upside-down-spectrum.png" alt="A screenshot example of upside-down MRS spectra"></p>
<p>Gannet has a routine that automatically phases spectra so that they
are not upside-down or otherwise out of phase. However, this routine can
fail. It is best to contact the developers for assistance to resolve the
problem. A possible, but not infallible, solution is to add the
following line of code to <code>GannetLoad.m</code> after the function
<code>PhaseCorrection.m</code> is run for global zero-order phase
correction (around line 400):</p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>MRS_struct.fids.data <span class="op">=</span> <span class="op">-</span>MRS_struct.fids.data<span class="op">;</span></span></code></pre></div>
</div>
</div>
<div id="errors" class="section level2 hasAnchor">
<h2 class="hasAnchor">Errors<a href="#errors" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<div
id="you-have-issues-with-spm-mex-files-on-macos-catalina-big-sur-monterey-ventura"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>1. You have issues with SPM MEX files on
macOS Catalina, Big Sur, Monterey, Ventura</strong><a
href="#you-have-issues-with-spm-mex-files-on-macos-catalina-big-sur-monterey-ventura"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>Specifically:</p>
<div class="sourceCode" id="cb2"><pre
class="sourceCode default"><code class="sourceCode default"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>"*.mexmaci64" cannot be opened because the developer cannot be verified. macOS cannot verify that this app is free from malware.</span></code></pre></div>
<p>or</p>
<div class="sourceCode" id="cb3"><pre
class="sourceCode default"><code class="sourceCode default"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>Code signature not valid for use in process using Library Validation: library load disallowed by system policy.</span></code></pre></div>
<p>Please visit the
<a href="https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)#macOS_Catalina,_Big_Sur,_Monterey,_Ventura" target="_blank">SPM
Wikibooks page</a> for troubleshooting.</p>
</div>
<div id="matlab-says-my-structural-image-does-not-exist"
class="section level4 hasAnchor">
<h4 class="hasAnchor"><strong>2. MATLAB says my structural image does
not exist</strong><a
href="#matlab-says-my-structural-image-does-not-exist"
class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>For example:</p>
<div class="sourceCode" id="cb4"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a>Error using spm_vol<span class="op">></span>spm_vol_hdr (<span class="fu">line</span> <span class="fl">80</span>)</span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a>File “image1.nii” does <span class="fu">not</span> exist.</span>
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a></span>
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a>Error in spm_vol (<span class="fu">line</span> <span class="fl">61</span>)</span>
<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a><span class="op">**</span> v <span class="op">=</span> spm_vol_hdr(<span class="fu">deblank</span>(P(<span class="fu">i</span><span class="op">,:</span>)))<span class="op">;**</span></span>
<span id="cb4-6"><a href="#cb4-6" tabindex="-1"></a></span>
<span id="cb4-7"><a href="#cb4-7" tabindex="-1"></a>Error in GannetMask_SiemensTWIX (<span class="fu">line</span> <span class="fl">110</span>)</span>
<span id="cb4-8"><a href="#cb4-8" tabindex="-1"></a>V <span class="op">=</span> spm_vol(nii_file)<span class="op">;</span></span>
<span id="cb4-9"><a href="#cb4-9" tabindex="-1"></a></span>
<span id="cb4-10"><a href="#cb4-10" tabindex="-1"></a>Error in GannetCoRegister (<span class="fu">line</span> <span class="fl">74</span>)</span>
<span id="cb4-11"><a href="#cb4-11" tabindex="-1"></a><span class="op">**</span> MRS_struct <span class="op">=</span> GannetMask_SiemensTWIX(fname<span class="op">,</span> nii_name{ii}<span class="op">,</span> MRS_struct<span class="op">,</span> ii<span class="op">,</span> vox<span class="op">,</span> kk)<span class="op">;**</span></span>
<span id="cb4-12"><a href="#cb4-12" tabindex="-1"></a></span>
<span id="cb4-13"><a href="#cb4-13" tabindex="-1"></a>Error in gannetcode (<span class="fu">line</span> <span class="fl">19</span>)</span>
<span id="cb4-14"><a href="#cb4-14" tabindex="-1"></a><span class="op">**</span> MRS_struct <span class="op">=</span> GannetCoRegister(MRS_struct<span class="op">,</span>{‘image1.nii’})<span class="op">;**</span></span></code></pre></div>
<p>A possible fix for this is to input filenames using their full path.
So, instead of <code>{'image1.nii'}</code>, input
<code>{'/Users/username/Documents/my_project/data/image1.nii'}</code>.</p>
</div>
</div>
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</div>
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selectors: "h1,h2",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = false;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>