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additional-tools.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Additional tools</title>
<script src="site_libs/header-attrs-2.28/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/lumen.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/navigation-1.1/sourceembed.js"></script>
<link href="site_libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="site_libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="site_libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
<!DOCTYPE html>
<link rel="shortcut icon" href="images/logo.png" />
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">
code {
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overflow: visible;
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</style>
<style type="text/css" data-origin="pandoc">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
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code.sourceCode > span { color: inherit; text-decoration: inherit; }
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@media print {
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position: relative; left: -1em; text-align: right; vertical-align: baseline;
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color: #aaaaaa;
}
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div.sourceCode
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@media screen {
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code span.dt { color: #204a87; } /* DataType */
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code span.er { color: #a40000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
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code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
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code span.ss { color: #4e9a06; } /* SpecialString */
code span.st { color: #4e9a06; } /* String */
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code span.vs { color: #4e9a06; } /* VerbatimString */
code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
var sheets = document.styleSheets;
for (var i = 0; i < sheets.length; i++) {
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
var j = 0;
while (j < rules.length) {
var rule = rules[j];
// check if there is a div.sourceCode rule
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}
})();
</script>
<style type="text/css">
#rmd-source-code {
display: none;
}
</style>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark the anchor link active (and if it's in a dropdown, also mark that active)
var dropdown = menuAnchor.closest('li.dropdown');
if (window.bootstrap) { // Bootstrap 4+
menuAnchor.addClass('active');
dropdown.find('> .dropdown-toggle').addClass('active');
} else { // Bootstrap 3
menuAnchor.parent().addClass('active');
dropdown.addClass('active');
}
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258";
font-family: 'Glyphicons Halflings';
border: none;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Gannet</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="getting-started.html">Getting started</a>
</li>
<li>
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</li>
<li>
<a href="output-structure-attributes.html">Output structure attributes</a>
</li>
<li>
<a href="preprocessing.html">Preprocessing</a>
</li>
<li>
<a href="signal-modeling.html">Signal modeling</a>
</li>
<li>
<a href="data-quality-metrics.html">Data quality metrics</a>
</li>
<li>
<a href="quantification-tissue-correction.html">Quantification & tissue correction</a>
</li>
<li>
<a href="additional-tools.html">Additional tools</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="gannetpreinitialise-settings.html">GannetPreInitialise settings</a>
</li>
<li>
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</li>
<li>
<a href="joining-data-files.html">Joining data files</a>
</li>
</ul>
</li>
<li>
<a href="faq.html">FAQ</a>
</li>
<li>
<a href="release-notes.html">Release notes</a>
</li>
<li>
<a href="https://forum.mrshub.org/c/mrs-software/gannet/9">Forum</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/markmikkelsen/Gannet/issues">Report an issue</a>
</li>
<li>
<a href="https://github.com/markmikkelsen/Gannet">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
<li>
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<span class="fa fa-envelope fa-lg"></span>
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</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
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<div class="btn-group pull-right float-right">
<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
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</ul>
</div>
<h1 class="title toc-ignore">Additional tools</h1>
<h4 class="date">Last updated: October 14, 2024</h4>
</div>
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<p><br></p>
<p>In addition to the five core modules, Gannet comes with a few
additional tools that you may find useful.</p>
<div id="paperplot" class="section level2 hasAnchor">
<h2 class="hasAnchor">PaperPlot<a href="#paperplot"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><code>PaperPlot.m</code> will plot the difference spectra saved in
the Gannet output structure. The corresponding model fits optionally can
also be plotted. Users can choose to plot a single spectrum, a select
number of spectra, all spectra, or an average of all spectra with or
without the standard deviation. Multiple spectra will be overlaid in the
same figure. If data were acquired with HERMES, then each
Hadamard-combined difference spectrum will be plotted in a separate
subplot.</p>
<p>Type <code>help PaperPlot</code> in the MATLAB command window for
usage instructions.</p>
<p>To export plots at publication quality, consider using
<code>PaperPlot.m</code> with Yair Altman’s excellent
<a href="https://github.com/altmany/export_fig/" target="_blank">export_fig</a>
MATLAB toolbox. This toolbox is bundled with Gannet.</p>
<div id="example-usage" class="section level3 hasAnchor">
<h3 class="hasAnchor">Example usage<a href="#example-usage"
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>metab <span class="op">=</span> {<span class="st">'S01_GABA_68_act.sdat'</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="st">'S02_GABA_68_act.sdat'</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="st">'S03_GABA_68_act.sdat'</span>}<span class="op">;</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>water <span class="op">=</span> {<span class="st">'S01_GABA_68_ref.sdat'</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> <span class="st">'S02_GABA_68_ref.sdat'</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a> <span class="st">'S03_GABA_68_ref.sdat'</span>}<span class="op">;</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>MRS <span class="op">=</span> GannetLoad(metab<span class="op">,</span> water)<span class="op">;</span></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>MRS <span class="op">=</span> GannetFit(MRS)<span class="op">;</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>PaperPlot(MRS)<span class="op">;</span> <span class="co">% Use default settings</span></span></code></pre></div>
<p><img id="img_75" src="images/additional-tools/paperplot-1.png" alt="Example output of PaperPlot.m"></p>
<div class="sourceCode" id="cb2"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>PaperPlot(MRS<span class="op">,</span> <span class="st">'plotModel'</span><span class="op">,</span> <span class="fu">true</span>)<span class="op">;</span> <span class="co">% Overlay fit models</span></span></code></pre></div>
<p><img id="img_75" src="images/additional-tools/paperplot-2.png" alt="Example output of PaperPlot.m"></p>
<div class="sourceCode" id="cb3"><pre
class="sourceCode octave"><code class="sourceCode octave"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>PaperPlot(MRS<span class="op">,</span> <span class="st">'plotModel'</span><span class="op">,</span> <span class="fu">true</span><span class="op">,</span> <span class="st">'freqLim'</span><span class="op">,</span> [<span class="fl">2</span> <span class="fl">4.25</span>])<span class="op">;</span> <span class="co">% Overlay fit models and</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a> <span class="co">% set ppm limits to 2-4.25</span></span></code></pre></div>
<p><img id="img_75" src="images/additional-tools/paperplot-3.png" alt="Example output of PaperPlot.m"></p>
</div>
</div>
<div id="de-identification" class="section level2 hasAnchor">
<h2 class="hasAnchor">De-identification<a href="#de-identification"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>MRI examinations involving human volunteers routinely store sensitive
protected health information (PHI) and personally identifiable
information (PII) in the exported data files. It is of vital importance
to protect volunteers’ privacy. To comply with privacy legislation, you
need to ensure that the data you handle, process, and share is
appropriately and thoroughly de-identified, i.e., stripped of all
PHI/PII that allows the data to be linked to an individual. This is
particularly critical if you intend to share data outside your
institution.</p>
<p>Gannet includes several functions to remove PHI/PII from the most
commonly used file formats. Currently, we offer functions to remove
PHI/PII from GE P-files (*.7), Siemens TWIX (*.dat), Philips
(*.sdat/*.spar), and generic DICOM (*.dcm) files. We plan to add support
for other formats in the future.</p>
<p>Please
<a href="mailto:[email protected]?subject=[Gannet]%20<Please enter the subject of your query here>" target="_blank">contact
us</a> if you require a de-identification tool for a different
format.</p>
<p>Please note the following:</p>
<div class="warning">
<i class="fa fa-exclamation-circle" style="color: white"></i>
<ul>
<li>
Gannet does not remove PHI/PII from filenames; this is solely your
responsibility.
</li>
<li>
In addition to any PHI/PII in the header of structural image files, they
need to be defaced as well. Please use a skull-stripping tool (such as
the one implemented in FSL) or a defacing tool (e.g.,
<a href="https://github.com/poldracklab/pydeface" target="_blank" style="color:white"><u>pydeface</u></a>).
</li>
<li>
Per our
<a href="https://markmikkelsen.github.io/Gannet-docs/gannet-license.html" target="_blank" style="color:white"><u>software
license</u></a>, the Gannet developers are not liable for any failure of
our de-identification routines to remove PHI/PII from your data.
</li>
</ul>
</div>
<div id="how-to-de-identify-your-files"
class="section level3 hasAnchor">
<h3 class="hasAnchor">How to de-identify your files<a
href="#how-to-de-identify-your-files" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<p>The Gannet de-identification functions create de-identified copies of
the original data. The original files are not overwritten.</p>
<p><u>GE P-files, Siemens TWIX, and Philips SDAT</u></p>
<p>For GE P-files (*.7), Siemens TWIX (*.dat), and Philips
(*.sdat/*.spar) files, the Gannet functions <code>GEDeIdentify.m</code>,
<code>TWIXDeIdentify.m</code>, and <code>PhilipsDeIdentify.m</code>
create de-identified copies of the respective files, appended with
<code>_noID</code>. All three functions can either be run by themselves
(without any input arguments) to de-identify all relevant files within
the current directory or given a cell array of filenames that you want
to de-identify.</p>
<p><u>DICOM</u></p>
<p>Generic DICOM data usually feature many separate *.dcm files for each
acquisition. <code>DICOMDeIdentify.m</code> requires a top-level
directory containing subdirectories for each subject
(e.g. <code>S01/</code>, <code>S02/</code>, <code>S03/</code>, etc.)
that contain all DICOM files for the respective subjects. Running
<code>DICOMDeIdentify.m</code> from the top-level directory will create
a separate directory containing the de-identified files for each
subject, appended with <code>_anon</code>.</p>
</div>
<div id="list-of-phi-identifiers" class="section level3 hasAnchor">
<h3 class="hasAnchor">List of PHI identifiers<a
href="#list-of-phi-identifiers" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<p>The Gannet de-identification functions currently remove PHI/PII
identifiers defined by the
<a href="https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html" target="_blank">United
States Health Insurance Portability and Accountability Act (HIPAA)
Privacy Rule</a>. These include, but are not limited to:</p>
<ul>
<li>Names</li>
<li>Addresses</li>
<li>Dates, including birth date and examination date</li>
<li>Medical record numbers</li>
<li>Device identifiers and serial numbers</li>
</ul>
<p>Should the regulations in your country or institution require
additional information to be removed, please
<a href="mailto:[email protected]?subject=[Gannet]%20<Please enter the subject of your query here>" target="_blank">contact
us</a>.</p>
<div class="danger">
<p><i class="fa fa-exclamation-triangle" style="color: white"></i>
There is <u>no way</u> to retrieve PHI/PII from a de-identified file!
Make sure that you either retain a copy of the original file or that you
keep a separate record that uniquely links all necessary subject
information to the de-identified file.</p>
</div>
</div>
</div>
<div id="coregstandalone" class="section level2 hasAnchor">
<h2 class="hasAnchor">CoRegStandAlone<a href="#coregstandalone"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Gannet has a standalone routine for voxel co-registration and
segmentation that can be utilized with any single-voxel MRS dataset,
including non-edited data. <code>CoRegStandAlone.m</code> contains
simplified versions of <code>GannetLoad.m</code>,
<code>GannetCoRegister.m</code>, and <code>GannetSegment.m</code> to
parse geometrical information about voxel dimensions, positions, and
rotations.</p>
<p><code>CoRegStandAlone.m</code> supports the same input formats as the
main Gannet modules. Upon being called, it produces GannetCoRegister and
GannetSegment outputs for each provided dataset. However, the
GannetSegment output does not contain any quantitative information,
except for tissue composition (voxel tissue fractions of GM, WM, and
CSF).</p>
<p>The syntax is similar to <code>GannetLoad.m</code> syntax, where the
first cell array contains the MRS filenames and the second cell array
contains the respective NIfTI filenames:</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>MRS_struct <span class="op">=</span> CoRegStandAlone({<span class="st">'data1.dat'</span><span class="op">,</span> <span class="st">'data2.dat'</span>}<span class="op">,</span> {<span class="st">'structural1.nii'</span><span class="op">,</span> <span class="st">'structural2.nii'</span>})<span class="op">;</span></span></code></pre></div>
<p>Please note that the number of NIfTI files needs to match the number
of MRS data files; i.e., if you want to register <em>N</em> voxels to
the same structural image, you’ll need to replicate the name of the
NIfTI file <em>N</em> times.</p>
</div>
<div id="rmd-source-code">---
title: "Additional tools"
date: "Last updated: `r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    toc: TRUE
    toc_depth: 3
    toc_float:
      collapsed: FALSE
---

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

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

<br>

In addition to the five core modules, Gannet comes with a few additional tools that you may find useful.

## PaperPlot

`PaperPlot.m` will plot the difference spectra saved in the Gannet output structure. The corresponding model fits optionally can also be plotted. Users can choose to plot a single spectrum, a select number of spectra, all spectra, or an average of all spectra with or without the standard deviation. Multiple spectra will be overlaid in the same figure. If data were acquired with HERMES, then each Hadamard-combined difference spectrum will be plotted in a separate subplot.

Type `help PaperPlot` in the MATLAB command window for usage instructions.

To export plots at publication quality, consider using `PaperPlot.m` with Yair Altman's excellent <a href="https://github.com/altmany/export_fig/" target="_blank">export_fig</a> MATLAB toolbox. This toolbox is bundled with Gannet.

### Example usage

```{octave, eval = FALSE}
metab = {'S01_GABA_68_act.sdat'
         'S02_GABA_68_act.sdat'
         'S03_GABA_68_act.sdat'};
water = {'S01_GABA_68_ref.sdat'
         'S02_GABA_68_ref.sdat'
         'S03_GABA_68_ref.sdat'};

MRS = GannetLoad(metab, water);
MRS = GannetFit(MRS);

PaperPlot(MRS); % Use default settings
```

<img id="img_75" src="images/additional-tools/paperplot-1.png" alt="Example output of PaperPlot.m">

```{octave, eval = FALSE}
PaperPlot(MRS, 'plotModel', true); % Overlay fit models
```

<img id="img_75" src="images/additional-tools/paperplot-2.png" alt="Example output of PaperPlot.m">

```{octave, eval = FALSE}
PaperPlot(MRS, 'plotModel', true, 'freqLim', [2 4.25]); % Overlay fit models and
                                                        % set ppm limits to 2-4.25
```

<img id="img_75" src="images/additional-tools/paperplot-3.png" alt="Example output of PaperPlot.m">

## De-identification

MRI examinations involving human volunteers routinely store sensitive protected health information (PHI) and personally identifiable information (PII) in the exported data files. It is of vital importance to protect volunteers’ privacy. To comply with privacy legislation, you need to ensure that the data you handle, process, and share is appropriately and thoroughly de-identified, i.e., stripped of all PHI/PII that allows the data to be linked to an individual. This is particularly critical if you intend to share data outside your institution.

Gannet includes several functions to remove PHI/PII from the most commonly used file formats. Currently, we offer functions to remove PHI/PII from GE P-files (\*.7), Siemens TWIX (\*.dat), Philips (\*.sdat/\*.spar), and generic DICOM (\*.dcm) files. We plan to add support for other formats in the future.

Please <a href="mailto:mam4041@med.cornell.edu?subject=[Gannet]%20<Please enter the subject of your query here>" target="_blank">contact us</a> if you require a de-identification tool for a different format.

Please note the following:

::: warning
<i class="fa fa-exclamation-circle" style="color: white"></i>
<ul>
  <li>Gannet does not remove PHI/PII from filenames; this is solely your responsibility.</li>
  <li>In addition to any PHI/PII in the header of structural image files, they need to be defaced as well. Please use a skull-stripping tool (such as the one implemented in FSL) or a defacing tool (e.g., <a href="https://github.com/poldracklab/pydeface" target="_blank" style="color:white"><u>pydeface</u></a>).</li>
  <li>Per our <a href="https://markmikkelsen.github.io/Gannet-docs/gannet-license.html" target="_blank" style="color:white"><u>software license</u></a>, the Gannet developers are not liable for any failure of our de-identification routines to remove PHI/PII from your data.</li>
</ul>
:::

### How to de-identify your files

The Gannet de-identification functions create de-identified copies of the original data. The original files are not overwritten.

<u>GE P-files, Siemens TWIX, and Philips SDAT</u>

For GE P-files (\*.7), Siemens TWIX (\*.dat), and Philips (\*.sdat/\*.spar) files, the Gannet functions `GEDeIdentify.m`, `TWIXDeIdentify.m`, and `PhilipsDeIdentify.m` create de-identified copies of the respective files, appended with `_noID`. All three functions can either be run by themselves (without any input arguments) to de-identify all relevant files within the current directory or given a cell array of filenames that you want to de-identify.

<u>DICOM</u>

Generic DICOM data usually feature many separate \*.dcm files for each acquisition. `DICOMDeIdentify.m` requires a top-level directory containing subdirectories for each subject (e.g. `S01/`, `S02/`, `S03/`, etc.) that contain all DICOM files for the respective subjects. Running `DICOMDeIdentify.m` from the top-level directory will create a separate directory containing the de-identified files for each subject, appended with `_anon`.

### List of PHI identifiers

The Gannet de-identification functions currently remove PHI/PII identifiers defined by the <a href="https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html" target="_blank">United States Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule</a>. These include, but are not limited to:

- Names
- Addresses
- Dates, including birth date and examination date
- Medical record numbers
- Device identifiers and serial numbers

Should the regulations in your country or institution require additional information to be removed, please <a href="mailto:mam4041@med.cornell.edu?subject=[Gannet]%20<Please enter the subject of your query here>" target="_blank">contact us</a>.

::: danger
<i class="fa fa-exclamation-triangle" style="color: white"></i>&nbsp; There is <u>no way</u> to retrieve PHI/PII from a de-identified file! Make sure that you either retain a copy of the original file or that you keep a separate record that uniquely links all necessary subject information to the de-identified file.
:::

## CoRegStandAlone

Gannet has a standalone routine for voxel co-registration and segmentation that can be utilized with any single-voxel MRS dataset, including non-edited data. `CoRegStandAlone.m` contains simplified versions of `GannetLoad.m`, `GannetCoRegister.m`, and `GannetSegment.m` to parse geometrical information about voxel dimensions, positions, and rotations.

`CoRegStandAlone.m` supports the same input formats as the main Gannet modules. Upon being called, it produces GannetCoRegister and GannetSegment outputs for each provided dataset. However, the GannetSegment output does not contain any quantitative information, except for tissue composition (voxel tissue fractions of GM, WM, and CSF).

The syntax is similar to `GannetLoad.m` syntax, where the first cell array contains the MRS filenames and the second cell array contains the respective NIfTI filenames:

```{octave, eval = FALSE}
MRS_struct = CoRegStandAlone({'data1.dat', 'data2.dat'}, {'structural1.nii', 'structural2.nii'});
```

Please note that the number of NIfTI files needs to match the number of MRS data files; i.e., if you want to register _N_ voxels to the same structural image, you’ll need to replicate the name of the NIfTI file _N_ times.



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