-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
837 lines (761 loc) · 41.4 KB
/
index.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
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Gannet</title>
<script src="site_libs/header-attrs-2.26/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 { 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">Gannet</h1>
<h4 class="date">Last updated: May 07, 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">
/* This enables wrapping of code blocks */
pre.sourceCode code {
white-space: pre-wrap;
}
</style>
<p><br></p>
<p><img id="img_50" src="images/logo+title.png" alt="The Gannet logo"/></p>
<div class="release">
<h3>
Current stable release:
<a href="https://github.com/markmikkelsen/Gannet" target="_blank" class="badge badge-secondary">3.3.2</a>
</h3>
</div>
<div id="overview" class="section level2 hasAnchor">
<h2 class="hasAnchor">Overview<a href="#overview" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p>Gannet is a free, open-source MATLAB-based software toolkit for
analyzing edited single-voxel <sup>1</sup>H magnetic resonance
spectroscopy (MRS) data. Its largely automated functions cover all the
essential steps of modern MRS analysis:</p>
<ul>
<li>Loading raw data</li>
<li>Substantial preprocessing</li>
<li>Signal modeling</li>
<li>Voxel co-registration with structural MR images</li>
<li>Concentration estimation based on tissue composition</li>
</ul>
<p>Several existing software packages for MRS data analysis require
substantial user input or offer a wide selection of processing options.
In contrast, the philosophy behind Gannet is to provide users with a
complete automated pipeline without the need for significant user
input.</p>
<p>Additionally, as open-source software, advanced users have the
ability to modify the underlying routines for ad hoc purposes.</p>
</div>
<div id="installation" class="section level2 hasAnchor">
<h2 class="hasAnchor">Installation<a href="#installation"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="prerequisites" class="section level3 hasAnchor">
<h3 class="hasAnchor">Prerequisites<a href="#prerequisites"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Gannet runs in
<a href="https://mathworks.com/products/matlab.html" target="_blank">MATLAB</a>.
For best performance, we recommend using the latest release if possible.
Additionally, Gannet requires that the following MATLAB toolboxes are
installed:</p>
<ul>
<li>Image Processing</li>
<li>Optimization</li>
<li>Signal Processing</li>
<li>Statistics and Machine Learning</li>
</ul>
<p>You can check which toolboxes you have installed by typing
<code>ver</code> in the MATLAB command window. To install any missing
toolboxes, please follow these
<a href="https://mathworks.com/matlabcentral/answers/101885-how-do-i-install-additional-toolboxes-into-an-existing-installation-of-matlab" target="_blank">instructions</a>.</p>
<p>To run the voxel co-registration and structural image segmentation
modules,
<a href="https://www.fil.ion.ucl.ac.uk/spm/software/spm12/" target="_blank">SPM12</a>
must be installed.</p>
</div>
<div id="download" class="section level3 hasAnchor">
<h3 class="hasAnchor">Download<a href="#download" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<p>The simplest way to install Gannet is to download the latest source
code as a ZIP file from the
<a href="https://github.com/markmikkelsen/Gannet" target="_blank">GitHub
repository</a> and move the <code>Gannet-main/</code> directory into
your main MATLAB directory (or wherever else you wish).</p>
<p>Alternatively, Git users can clone the Gannet repository into a
directory of their choice:</p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode default"><code class="sourceCode default"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>git clone https://github.com/markmikkelsen/Gannet.git</span></code></pre></div>
<p>The development version of Gannet can be downloaded from the
<a href="https://github.com/markmikkelsen/Gannet/tree/dev" target="_blank">development
branch</a> on GitHub or by using the following git command if the
repository was cloned:</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>git checkout dev</span></code></pre></div>
<p>Stable releases can be found
<a href="https://github.com/markmikkelsen/Gannet/releases" target="_blank">here</a>.</p>
</div>
<div id="setup" class="section level3 hasAnchor">
<h3 class="hasAnchor">Setup<a href="#setup" class="anchor-section"
aria-label="Anchor link to header"></a></h3>
<p>Open the <em>Set Path</em> dialog box from the MATLAB menu (or run
the command <code>pathtool</code> in the Command Window), click <em>Add
with Subfolders…</em>, find the downloaded Gannet directory, and then
select it. When done, press <em>Save</em> to permanently save the Gannet
directory to MATLAB’s default search path.</p>
<p>SPM12 can be installed in the same manner after it has been
downloaded from the
<a href="https://www.fil.ion.ucl.ac.uk/spm/software/spm12/" target="_blank">SPM</a>
website.</p>
<div class="info">
<p><i class="fa fa-info-circle" style="color: white"></i> It is highly
recommended that you only add the main SPM12 directory
(<code>spm12/</code>) to your search path instead of including all the
subdirectories. This prevents function conflicts.</p>
</div>
<div class="warning">
<p><i class="fa fa-exclamation-circle" style="color: white"></i> If you
have
<a href="https://github.com/schorschinho/osprey" target="_blank" style="color:white"><u>Osprey</u></a>
also installed on your computer, please ensure that you either have all
the Gannet and SPM12 directories at the top of your search path or have
removed the Osprey directories from your search path. Gannet and Osprey
share several functions that can lead to conflicts that result in Gannet
not functioning correctly.</p>
</div>
</div>
</div>
<div id="compatibility" class="section level2 hasAnchor">
<h2 class="hasAnchor">Compatibility<a href="#compatibility"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Gannet is currently being developed in MATLAB R2024a in macOS 14
Sonoma (Apple silicon). While reasonable effort is made to ensure legacy
and cross-OS compatibility, an error-free user experience is not
guaranteed.</p>
</div>
<div id="supported-file-formats" class="section level2 hasAnchor">
<h2 class="hasAnchor">Supported file formats<a
href="#supported-file-formats" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p>At present, the following MRS data file formats are supported:</p>
<ul>
<li>DICOM (.dcm)</li>
<li>GE P-file (.7)</li>
<li>NIfTI-MRS (.nii[.gz])</li>
<li>Philips .data/.list</li>
<li>Philips .raw</li>
<li>Philips .sdat/.spar</li>
<li>Siemens DICOM (.ima)</li>
<li>Siemens .rda</li>
<li>Siemens TWIX (.dat)</li>
</ul>
<p>For creating and co-registering voxel masks, structural images need
to be in NIfTI format (DICOM files can also be used if processing GE
P-files).</p>
<div class="warning">
<p><i class="fa fa-exclamation-circle" style="color: white"></i> Philips
users: Do not use structural images exported using the
<em>fsl-nifti</em> option as this creates problems with co-registration
in Gannet.</p>
</div>
</div>
<div id="getting-help" class="section level2 hasAnchor">
<h2 class="hasAnchor">Getting help<a href="#getting-help"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>If you encounter any problems, please first check the Documentation
or <a
href="https://markmikkelsen.github.io/Gannet-docs/faq.html">FAQ</a> for
a solution.</p>
<p>Otherwise, you can post your query on the
<a href="https://forum.mrshub.org/c/mrs-software/gannet/9" target="_blank">Gannet
forum</a> on
<a href="https://mrshub.org/" target="_blank">MRSHub</a>.</p>
<p>The Gannet team can also be
<a href="mailto:[email protected]?subject=[Gannet]%20<Please enter the subject of your query here>" target="_blank">contacted</a>
directly. We will do our best to work with you to solve your issue.</p>
</div>
<div id="versioning" class="section level2 hasAnchor">
<h2 class="hasAnchor">Versioning<a href="#versioning"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Gannet uses a form of
<a href="https://semver.org/" target="_blank">semantic versioning</a> in
the style ‘x.x.x’ to mark code releases. Versioning is also conducted on
a module-specific basis using the style ‘YYMMDD’. That is, each Gannet
module has its own release version. Users should note that
module-specific versions sometimes are updated despite the semantic
version number remaining unchanged (typically for minor updates/bug
fixes).</p>
</div>
<div id="developers" class="section level2 hasAnchor">
<h2 class="hasAnchor">Developers<a href="#developers"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<ul>
<li>Richard Edden (Johns Hopkins University) - creator</li>
<li>Mark Mikkelsen (Weill Cornell Medicine) - lead developer</li>
<li>Georg Oeltzschner (Johns Hopkins University) - contributor</li>
<li>Muhammad Saleh (Children’s Hospital of Philadelphia) -
contributor</li>
<li>C. John Evans (Cardiff University) - contributor</li>
<li>Ashley Harris (University of Calgary) - contributor</li>
<li>Nicolaas Puts (King’s College London) - contributor</li>
</ul>
</div>
<div id="license-and-citing-gannet" class="section level2 hasAnchor">
<h2 class="hasAnchor">License and citing Gannet<a
href="#license-and-citing-gannet" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p>This software is licensed under an open-source <a
href="https://markmikkelsen.github.io/Gannet-docs/gannet-license.html">BSD-3-Clause
License</a>. Should you disseminate material that made use of Gannet,
please cite the following publications, as appropriate:</p>
<ul>
<li>Edden RAE, Puts NAJ, Harris AD, Barker PB, Evans CJ.
<a href="https://doi.org/10.1002/jmri.24478" target="_blank">Gannet: A
batch-processing tool for the quantitative analysis of
gamma-aminobutyric acid-edited MR spectroscopy spectra.</a> <em>Journal
of Magnetic Resonance Imaging</em>. 2014;40(6):1445–1452</li>
</ul>
<p><strong>If you perform frequency-and-phase correction (FPC)
using:</strong></p>
<p>Robust spectral registration (<code>RobustSpecReg</code>):</p>
<ul>
<li>Mikkelsen M, Tapper S, Near J, Mostofsky SH, Puts NAJ, Edden RAE.
<a href="https://doi.org/10.1002/nbm.4368" target="_blank">Correcting
frequency and phase offsets in MRS data using robust spectral
registration.</a> <em>NMR in Biomedicine</em>. 2020;33(10):e4368</li>
</ul>
<p>multi-step FPC (<code>SpecRegHERMES</code>):</p>
<ul>
<li>Mikkelsen M, Saleh MG, Near J, et
al. <a href="https://doi.org/10.1002/mrm.27027" target="_blank">Frequency
and phase correction for multiplexed edited MRS of GABA and
glutathione.</a> <em>Magnetic Resonance in Medicine</em>.
2018;80(1):21–28</li>
</ul>
<p>or spectral registration (<code>SpecReg</code>):</p>
<ul>
<li>Near J, Edden R, Evans CJ, Paquin R, Harris A, Jezzard P.
<a href="https://doi.org/10.1002/mrm.25094" target="_blank">Frequency
and phase drift correction of magnetic resonance spectroscopy data by
spectral registration in the time domain.</a> <em>Magnetic Resonance in
Medicine</em>. 2015;73(1):44–50</li>
</ul>
<p><strong>If you perform voxel co-registration:</strong></p>
<ul>
<li>Please acknowledge the use of SPM12. You may also link/cite the
<a href="https://www.fil.ion.ucl.ac.uk/spm/software/spm12/" target="_blank">SPM12
website</a>.</li>
</ul>
<p><strong>If you perform tissue segmentation:</strong></p>
<ul>
<li>Ashburner J, Friston KJ.
<a href="https://doi.org/10.1016/j.neuroimage.2005.02.018" target="_blank">Unified
segmentation.</a> <em>NeuroImage</em>. 2005;26(3):839–851</li>
</ul>
<p><strong>If you report water-referenced, tissue-corrected metabolite
measurements using:</strong></p>
<p>The Harris et al. method:</p>
<ul>
<li>Harris AD, Puts NAJ, Edden RAE.
<a href="https://doi.org/10.1002/jmri.24903" target="_blank">Tissue
correction for GABA-edited MRS: Considerations of voxel composition,
tissue segmentation, and tissue relaxations.</a> <em>Journal of Magnetic
Resonance Imaging</em>. 2015;42(5):1431–1440</li>
</ul>
<p>or the Gasparovic et al. method:</p>
<ul>
<li>Gasparovic C, Song T, Devier D, et
al. <a href="https://doi.org/10.1002/mrm.20901" target="_blank">Use of
tissue water as a concentration reference for proton spectroscopic
imaging.</a> <em>Magnetic Resonance in Medicine</em>.
2006;55(6):1219–1226</li>
</ul>
</div>
<div id="acknowledgments" class="section level2 hasAnchor">
<h2 class="hasAnchor">Acknowledgments<a href="#acknowledgments"
class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>The development and dissemination of Gannet has been supported by the
following NIH grants:</p>
<ul>
<li>R01 EB016089</li>
<li>R01 EB023963</li>
<li>P41 EB015909</li>
<li>K99 EB028828</li>
<li>R01 MH106564</li>
<li>R21 MH098228</li>
<li>R21 NS077300</li>
<li>R01 MH096263</li>
</ul>
<p>We wish to thank the following individuals for their direct or
indirect contributions:</p>
<ul>
<li>Yair Altman (Undocumented Matlab)</li>
<li>Peter Barker (Johns Hopkins University)</li>
<li>Alex Craven (University of Bergen)</li>
<li>Philipp Ehses (Max Planck Institute for Biological Cybernetics)</li>
<li>Robin de Graaf (Yale School of Medicine)</li>
<li>Xiangrui Li (Ohio State University)</li>
<li>Jamie Near (McGill University)</li>
<li>Ralph Noeske (GE Healthcare)</li>
<li>Wouter Potters (UMC Amsterdam)</li>
<li>Jan Simon (Heidelberg)</li>
</ul>
</div>
<div id="rmd-source-code">---
title: "Gannet"
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}
/* This enables wrapping of code blocks */
pre.sourceCode code {
  white-space: pre-wrap;
}
```

<br>

<img id="img_50" src="images/logo+title.png" alt="The Gannet logo"/>

::: release
<h3>Current stable release: <a href="https://github.com/markmikkelsen/Gannet" target="_blank" class="badge badge-secondary">3.3.2</a></h3>
:::

## Overview

Gannet is a free, open-source MATLAB-based software toolkit for analyzing edited single-voxel ^1^H magnetic resonance spectroscopy (MRS) data. Its largely automated functions cover all the essential steps of modern MRS analysis:

-   Loading raw data
-   Substantial preprocessing
-   Signal modeling
-   Voxel co-registration with structural MR images
-   Concentration estimation based on tissue composition

Several existing software packages for MRS data analysis require substantial user input or offer a wide selection of processing options. In contrast, the philosophy behind Gannet is to provide users with a complete automated pipeline without the need for significant user input.

Additionally, as open-source software, advanced users have the ability to modify the underlying routines for ad hoc purposes.

## Installation

### Prerequisites

Gannet runs in <a href="https://mathworks.com/products/matlab.html" target="_blank">MATLAB</a>. For best performance, we recommend using the latest release if possible. Additionally, Gannet requires that the following MATLAB toolboxes are installed:

-   Image Processing
-   Optimization
-   Signal Processing
-   Statistics and Machine Learning

You can check which toolboxes you have installed by typing `ver` in the MATLAB command window. To install any missing toolboxes, please follow these <a href="https://mathworks.com/matlabcentral/answers/101885-how-do-i-install-additional-toolboxes-into-an-existing-installation-of-matlab" target="_blank">instructions</a>.

To run the voxel co-registration and structural image segmentation modules, <a href="https://www.fil.ion.ucl.ac.uk/spm/software/spm12/" target="_blank">SPM12</a> must be installed.

### Download

The simplest way to install Gannet is to download the latest source code as a ZIP file from the <a href="https://github.com/markmikkelsen/Gannet" target="_blank">GitHub repository</a> and move the `Gannet-main/` directory into your main MATLAB directory (or wherever else you wish).

Alternatively, Git users can clone the Gannet repository into a directory of their choice:

```{verbatim, eval = FALSE}
git clone https://github.com/markmikkelsen/Gannet.git
```

The development version of Gannet can be downloaded from the <a href="https://github.com/markmikkelsen/Gannet/tree/dev" target="_blank">development branch</a> on GitHub or by using the following git command if the repository was cloned:

```{verbatim, eval = FALSE}
git checkout dev
```

Stable releases can be found <a href="https://github.com/markmikkelsen/Gannet/releases" target="_blank">here</a>.

### Setup

Open the *Set Path* dialog box from the MATLAB menu (or run the command `pathtool` in the Command Window), click *Add with Subfolders...*, find the downloaded Gannet directory, and then select it. When done, press *Save* to permanently save the Gannet directory to MATLAB's default search path.

SPM12 can be installed in the same manner after it has been downloaded from the <a href="https://www.fil.ion.ucl.ac.uk/spm/software/spm12/" target="_blank">SPM</a> website.

::: info
<i class="fa fa-info-circle" style="color: white"></i> It is highly recommended that you only add the main SPM12 directory (`spm12/`) to your search path instead of including all the subdirectories. This prevents function conflicts.
:::

::: warning
<i class="fa fa-exclamation-circle" style="color: white"></i> If you have <a href="https://github.com/schorschinho/osprey" target="_blank" style="color:white"><u>Osprey</u></a> also installed on your computer, please ensure that you either have all the Gannet and SPM12 directories at the top of your search path or have removed the Osprey directories from your search path. Gannet and Osprey share several functions that can lead to conflicts that result in Gannet not functioning correctly.
:::

## Compatibility

Gannet is currently being developed in MATLAB R2024a in macOS 14 Sonoma (Apple silicon). While reasonable effort is made to ensure legacy and cross-OS compatibility, an error-free user experience is not guaranteed.

## Supported file formats

At present, the following MRS data file formats are supported:

- DICOM (.dcm)
- GE P-file (.7)
- NIfTI-MRS (.nii[.gz])
- Philips .data/.list
- Philips .raw
- Philips .sdat/.spar
- Siemens DICOM (.ima)
- Siemens .rda
- Siemens TWIX (.dat)

For creating and co-registering voxel masks, structural images need to be in NIfTI format (DICOM files can also be used if processing GE P-files).

::: warning
<i class="fa fa-exclamation-circle" style="color: white"></i> Philips users: Do not use structural images exported using the *fsl-nifti* option as this creates problems with co-registration in Gannet.
:::

## Getting help

If you encounter any problems, please first check the Documentation or [FAQ](https://markmikkelsen.github.io/Gannet-docs/faq.html) for a solution.

Otherwise, you can post your query on the <a href="https://forum.mrshub.org/c/mrs-software/gannet/9" target="_blank">Gannet forum</a> on <a href="https://mrshub.org/" target="_blank">MRSHub</a>.

The Gannet team can also be <a href="mailto:mam4041@med.cornell.edu?subject=[Gannet]%20<Please enter the subject of your query here>" target="_blank">contacted</a> directly. We will do our best to work with you to solve your issue.

## Versioning

Gannet uses a form of <a href="https://semver.org/" target="_blank">semantic versioning</a> in the style 'x.x.x' to mark code releases. Versioning is also conducted on a module-specific basis using the style 'YYMMDD'. That is, each Gannet module has its own release version. Users should note that module-specific versions sometimes are updated despite the semantic version number remaining unchanged (typically for minor updates/bug fixes).

## Developers

- Richard Edden (Johns Hopkins University) - creator
- Mark Mikkelsen (Weill Cornell Medicine) - lead developer
- Georg Oeltzschner (Johns Hopkins University) - contributor
- Muhammad Saleh (Children's Hospital of Philadelphia) - contributor
- C. John Evans (Cardiff University) - contributor
- Ashley Harris (University of Calgary) - contributor
- Nicolaas Puts (King's College London) - contributor

## License and citing Gannet

This software is licensed under an open-source [BSD-3-Clause License](https://markmikkelsen.github.io/Gannet-docs/gannet-license.html). Should you disseminate material that made use of Gannet, please cite the following publications, as appropriate:

- Edden RAE, Puts NAJ, Harris AD, Barker PB, Evans CJ. <a href="https://doi.org/10.1002/jmri.24478" target="_blank">Gannet: A batch-processing tool for the quantitative analysis of gamma-aminobutyric acid-edited MR spectroscopy spectra.</a> *Journal of Magnetic Resonance Imaging*. 2014;40(6):1445--1452

**If you perform frequency-and-phase correction (FPC) using:**

Robust spectral registration (`RobustSpecReg`):

- Mikkelsen M, Tapper S, Near J, Mostofsky SH, Puts NAJ, Edden RAE. <a href="https://doi.org/10.1002/nbm.4368" target="_blank">Correcting frequency and phase offsets in MRS data using robust spectral registration.</a> *NMR in Biomedicine*. 2020;33(10):e4368

multi-step FPC (`SpecRegHERMES`):

- Mikkelsen M, Saleh MG, Near J, et al. <a href="https://doi.org/10.1002/mrm.27027" target="_blank">Frequency and phase correction for multiplexed edited MRS of GABA and glutathione.</a> *Magnetic Resonance in Medicine*. 2018;80(1):21--28

or spectral registration (`SpecReg`):

- Near J, Edden R, Evans CJ, Paquin R, Harris A, Jezzard P. <a href="https://doi.org/10.1002/mrm.25094" target="_blank">Frequency and phase drift correction of magnetic resonance spectroscopy data by spectral registration in the time domain.</a> *Magnetic Resonance in Medicine*. 2015;73(1):44--50

**If you perform voxel co-registration:**

- Please acknowledge the use of SPM12. You may also link/cite the <a href="https://www.fil.ion.ucl.ac.uk/spm/software/spm12/" target="_blank">SPM12 website</a>.

**If you perform tissue segmentation:**

- Ashburner J, Friston KJ. <a href="https://doi.org/10.1016/j.neuroimage.2005.02.018" target="_blank">Unified segmentation.</a> *NeuroImage*. 2005;26(3):839--851

**If you report water-referenced, tissue-corrected metabolite measurements using:**

The Harris et al. method:

- Harris AD, Puts NAJ, Edden RAE. <a href="https://doi.org/10.1002/jmri.24903" target="_blank">Tissue correction for GABA-edited MRS: Considerations of voxel composition, tissue segmentation, and tissue relaxations.</a> *Journal of Magnetic Resonance Imaging*. 2015;42(5):1431--1440

or the Gasparovic et al. method:

- Gasparovic C, Song T, Devier D, et al. <a href="https://doi.org/10.1002/mrm.20901" target="_blank">Use of tissue water as a concentration reference for proton spectroscopic imaging.</a> *Magnetic Resonance in Medicine*. 2006;55(6):1219--1226

## Acknowledgments

The development and dissemination of Gannet has been supported by the following NIH grants:

- R01 EB016089
- R01 EB023963
- P41 EB015909
- K99 EB028828
- R01 MH106564
- R21 MH098228
- R21 NS077300
- R01 MH096263

We wish to thank the following individuals for their direct or indirect contributions:

- Yair Altman (Undocumented Matlab)
- Peter Barker (Johns Hopkins University)
- Alex Craven (University of Bergen)
- Philipp Ehses (Max Planck Institute for Biological Cybernetics)
- Robin de Graaf (Yale School of Medicine)
- Xiangrui Li (Ohio State University)
- Jamie Near (McGill University)
- Ralph Noeske (GE Healthcare)
- Wouter Potters (UMC Amsterdam)
- Jan Simon (Heidelberg)



</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("index.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>