-
Notifications
You must be signed in to change notification settings - Fork 0
/
gannetpreinitialise-settings.html
707 lines (631 loc) · 58.3 KB
/
gannetpreinitialise-settings.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>GannetPreInitialise settings</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/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 {
white-space: pre;
}
.sourceCode {
overflow: visible;
}
</style>
<style type="text/css" data-origin="pandoc">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ background-color: #f8f8f8; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ef2929; } /* Alert */
code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #204a87; } /* Attribute */
code span.bn { color: #0000cf; } /* BaseN */
code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4e9a06; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #8f5902; font-style: italic; } /* Comment */
code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
code span.dt { color: #204a87; } /* DataType */
code span.dv { color: #0000cf; } /* DecVal */
code span.er { color: #a40000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #0000cf; } /* Float */
code span.fu { color: #204a87; font-weight: bold; } /* Function */
code span.im { } /* Import */
code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
code span.ot { color: #8f5902; } /* Other */
code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
code span.sc { color: #ce5c00; font-weight: bold; } /* SpecialChar */
code span.ss { color: #4e9a06; } /* SpecialString */
code span.st { color: #4e9a06; } /* String */
code span.va { color: #000000; } /* Variable */
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
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
j++;
continue;
}
var style = rule.style.cssText;
// check if color or background-color is set
if (rule.style.color === '' && rule.style.backgroundColor === '') {
j++;
continue;
}
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
}
}
})();
</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>
</head>
<body>
<div class="container-fluid main-container">
<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">
Documentation
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="getting-started.html">Getting started</a>
</li>
<li>
<a href="reference.html">Reference</a>
</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">
Examples
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="gannetpreinitialise-settings.html">GannetPreInitialise settings</a>
</li>
<li>
<a href="batch-script.html">Batch processing script</a>
</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>
<a href="mailto:[email protected]?subject=[Gannet]%20<Please enter the subject of your query here>">
<span class="fa fa-envelope fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<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>
<ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
<li><a id="rmd-download-source" href="#">Download Rmd</a></li>
</ul>
</div>
<h1 class="title toc-ignore">GannetPreInitialise settings</h1>
<h4 class="date">Last updated: October 14, 2024</h4>
</div>
<button onclick="topFunction()" id="myBtn" title="Go to top">
Back to top
</button>
<script>
//Get the button
var mybutton = document.getElementById("myBtn");
// When the user scrolls down 20px from the top of the document, show the button
window.onscroll = function() {scrollFunction()};
function scrollFunction() {
if (document.body.scrollTop > 20 || document.documentElement.scrollTop > 20) {
mybutton.style.display = "block";
} else {
mybutton.style.display = "none";
}
}
// When the user clicks on the button, scroll to the top of the document
function topFunction() {
document.body.scrollTop = 0;
document.documentElement.scrollTop = 0;
}
</script>
<style type="text/css">
body .main-container {
max-width: 1200px;
}
</style>
<p><br></p>
<div class="warning">
<p><i class="fa fa-exclamation-circle" style="color: white"></i> These
examples were created in release 3.3.0. Take care copy-pasting these
examples into your version of <code>GannetPreInitialise.m</code>. You
may be using a different release that has older/newer variables that
could result in an error during the analysis pipeline.</p>
</div>
<div id="section"
class="section level2 tabset tabset-fade tabset-pills">
<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
```



</div>
<!DOCTYPE html>
<br>
<hr>
<p style="text-align: right;">Built with <a href="https://rmarkdown.rstudio.com/" target="_blank">R Markdown</a> in <a
href="https://posit.co/products/open-source/rstudio/" target="_blank">RStudio</a>
<br>
</p>
<p style="text-align: right;">Copyright © 2020–2024, Mark Mikkelsen <a
href="https://creativecommons.org/licenses/by/4.0" target="_blank"><img id="cc"
style="height:22px!important;margin-left: 3px;vertical-align:text-bottom;" src="images/license/cc-xlarge.png"><img
id="cc" style="height:22px!important;margin-left: 3px;vertical-align:text-bottom;"
src="images/license/by-xlarge.png"></a>
</p>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
window.initializeSourceEmbed("gannetpreinitialise-settings.Rmd");
});
</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>