-
Notifications
You must be signed in to change notification settings - Fork 0
/
release-notes.html
1137 lines (1041 loc) · 66.2 KB
/
release-notes.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
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Release notes</title>
<script src="site_libs/header-attrs-2.28/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/lumen.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/navigation-1.1/sourceembed.js"></script>
<link href="site_libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="site_libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="site_libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
<!DOCTYPE html>
<link rel="shortcut icon" href="images/logo.png" />
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">
#rmd-source-code {
display: none;
}
</style>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark the anchor link active (and if it's in a dropdown, also mark that active)
var dropdown = menuAnchor.closest('li.dropdown');
if (window.bootstrap) { // Bootstrap 4+
menuAnchor.addClass('active');
dropdown.find('> .dropdown-toggle').addClass('active');
} else { // Bootstrap 3
menuAnchor.parent().addClass('active');
dropdown.addClass('active');
}
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258";
font-family: 'Glyphicons Halflings';
border: none;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Gannet</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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">Release notes</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>
<p><br></p>
<p>This page lists the stable releases of Gannet since v3.1.3. All
releases can be found on GitHub
<a href="https://github.com/markmikkelsen/Gannet/releases" target="_blank">here</a>
and
<a href="https://github.com/richardedden/Gannet3.1/releases" target="_blank">here</a>.
The development version of Gannet can be found
<a href="https://github.com/markmikkelsen/Gannet/tree/dev" target="_blank">here</a>.
For a more comprehensive list of changes to the current main version,
see the commits logged on GitHub
<a href="https://github.com/markmikkelsen/Gannet/commits/main" target="_blank">here</a>.</p>
<div id="section" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.3.2<a href="#section" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2023-08-02</span></p>
<div id="major-changes" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Rewrote <code>SiemensRead.m</code> to reduce code length</li>
</ul>
</div>
<div id="minor-changes" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Updated <code>DICOMRead.m</code>, including to support Siemens XA30
data</li>
<li>Updated <code>SpectralRegistrationHERMES.m</code>
<ul>
<li>SNR limit is now estimated as in
<code>RobustSpectralRegistration.m</code></li>
<li>Bug fix for indexing for output saved from maximum likelihood
estimation</li>
</ul></li>
<li>Updated <code>dicm2nii</code> to version 2023.03.16</li>
<li>Updated <code>export_fig</code> to v3.40</li>
<li>Added Gannet documentation website URL to error dialog box</li>
<li>Changed the way path names are printed in error dialog box</li>
<li>Turned off iteration limit warning in <code>FitChoCr.m</code></li>
<li>Updated <code>UpdateGannet.m</code> to ensure all sub-directories
are added to the search path after updating</li>
<li>Added issue templates (in <code>.github/ISSUE_TEMPLATE</code>) for
blank issues, bug reports, and feature requests</li>
<li>Refined alignment of text/logos in output figures
<ul>
<li>The units used for displaying textual results are now normalized to
fit to any subplot dimension</li>
<li>The textual results in the <code>GannetCoRegister</code>,
<code>GannetSegment</code>, <code>CoReg</code>, and <code>Seg</code>
output figures are now correctly centered</li>
</ul></li>
<li>The weighted signal averaging method used is now saved in the
structure output</li>
<li>The weighting factors calculated when applying weighted signal
averaging are also now saved in the output</li>
<li>Updated <code>SavePDF.m</code> such that when appending PDFs using
<code>export_fig</code>, the figure size will now be equivalent in
pixels on Windows and Mac systems</li>
<li>Updated <code>NIfTIMRSRead.m</code></li>
<li>Updated <code>README.md</code></li>
<li>Updated <code>GannetFitPhantom.m</code></li>
<li>Removed redundant global frequency shift in
<code>RobustSpectralRegistration.m</code></li>
<li>The z-standardized MSEs calculated in the spectral registration
subroutines are now saved in the structure output</li>
<li>Updated <code>GannetVersion.m</code> to also output version numbers
of Gannet modules</li>
<li>A warning is now printed when users process Siemens .rda data
encouraging them to instead use TWIX (.dat) data</li>
<li>Added support for GE P-file header revision 30
(<a href="https://github.com/markmikkelsen/Gannet/issues/28" target="_blank">#28</a>)</li>
<li>MANY COSMETIC CHANGES</li>
</ul>
</div>
<div id="bug-fixes" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Bug fix for special character <code>\</code> in Windows file path
names printed in the error dialog box</li>
<li>Fixed bug in <code>GannetMask_NIfTI.m</code> where the co-registered
MRS voxel was incorrectly flipped in the <code>GannetCoRegister</code>
output figure</li>
<li>Fixed bug in <code>GannetQuantify.m</code> where the alpha value was
incorrectly being printed multiple times when multiple were run in
batch</li>
<li>Added fix in <code>VersionCheck.m</code> so that when users have
limited or restricted internet access, an error is avoided
(<a href="https://github.com/markmikkelsen/Gannet/pull/27" target="_blank">#27</a>)
- thanks <a href="https://github.com/alexcraven" target="_blank"><span
class="citation">@alexcraven</span></a>!</li>
</ul>
</div>
</div>
<div id="section-1" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.3.1<a href="#section-1" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2023-03-14</span></p>
<div id="new-features" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Compressed NIfTI files (*.nii.gz) are now fully supported</li>
<li>Gannet now fully quantifies metabolite levels for Cr, Cho, and NAA
(estimated from the OFF spectrum)</li>
</ul>
</div>
<div id="major-changes-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Moved local signal model functions out of <code>GannetFit.m</code>
and into their own files:
<ul>
<li><code>BaselineModel.m</code></li>
<li><code>CalcIU.m</code></li>
<li><code>DoubleGaussModel.m</code></li>
<li><code>EtOHModel.m</code></li>
<li><code>GABAGlxModel.m</code></li>
<li><code>GaussModel.m</code></li>
<li><code>LorentzGaussModel.m</code></li>
<li><code>LorentzGaussModelP.m</code></li>
</ul></li>
<li>Added <code>GetFullPath.m</code>; Gannet now will find the full path
of input files by default</li>
<li>Renamed some of the data-loading functions</li>
</ul>
</div>
<div id="minor-changes-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added a check in <code>GannetQuantify.m</code> for datasets without
water references; <code>GannetQuantify.m</code> will not run if no water
references are present</li>
<li>Added a check in <code>GannetCoRegister.m</code> to ensure all
structural image files can be found</li>
<li>Updated <code>export_fig</code> to v3.33</li>
<li>Updated <code>dicm2nii</code> to version 2023.03.08</li>
<li>Updated <code>LICENSE</code> and <code>README.md</code></li>
<li>Updated <code>ExportToCSV.m</code></li>
<li>Updated <code>CoRegStandAlone</code> functions</li>
<li>Replaced use of <code>1i</code> with <code>complex()</code></li>
<li>Removed unused variable <code>T1max</code></li>
<li>Removed unnecessary <code>ones()</code> parameter in
<code>LorentzModel.m</code> and <code>TwoLorentzModel.m</code></li>
<li>Philips *.spar file extension is no longer saved in the output
structure</li>
<li>Removed calculation of <code>df</code> in <code>GannetLoad.m</code>;
added <code>dt</code> in its place</li>
<li>Exported CSV files will no longer be overwritten if a CSV file of
the same name already exists in the output directory; instead, a new
file is created and appended with an integer</li>
<li>Added new output structure attribute <code>nrows_water</code></li>
<li>Reordered structure subfields for metabolites in
<code>GannetFit.m</code> and <code>ExportToCSV.m</code></li>
<li>Shifted Gannet logo and version number in PDF outputs slightly to
the right</li>
<li>Alpha values are now included in exported CSV files</li>
<li>Replaced the Gannet logo with a PNG version</li>
<li>MANY COSMETIC CHANGES</li>
</ul>
</div>
<div id="bug-fixes-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added a check for letter case of *.dcm and *.ima files in
<code>DICOMRead.m</code> and <code>SiemensDICOMRead.m</code>
(<code>dir()</code> is case-sensitive in Linux)</li>
<li>Added a fix to avoid an error where MATLAB tried to close figures
following an unrelated internal error, but no figures were created</li>
<li>Fixed a bug in <code>NIfTIMRSRead.m</code> that led to an error if
the <code>Manufacturer</code> field is not found in the data file
header</li>
<li>If <code>export_fig.m</code> cannot be found on the search path and
<code>append</code> has been flagged in
<code>GannetPreInitialise.m</code>, it is made clear to the user that
PDFs will be saved separately</li>
<li>Fixed bugs in <code>AlignUsingH2O.m</code></li>
<li>Fixed a bug in <code>SiemensDICOMRead.m</code> where an error
occurred if <code>centerFreq</code> is not found in the data file
header</li>
</ul>
</div>
</div>
<div id="section-2" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.3.0<a href="#section-2" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2022-10-22</span></p>
<div id="new-features-1" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features-1"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added functionality to read NIfTI-MRS files
(<a href="https://onlinelibrary.wiley.com/doi/10.1002/mrm.29418" target="_blank">Clarke
et al., MRM, 2022</a>) (<code>NIfTIMRSRead.m</code>); includes
additional new function <code>GannetMask_NIfTI.m</code> for voxel
co-registration</li>
<li>Added support for Utah Siemens MEGA-PRESS sequence (DICOM
files)</li>
<li>Added support for CMRR PRESS data (DICOM files)</li>
<li>Added support for Siemens XA30 sequence as provided by JHU</li>
<li>Changed <code>README</code> to <code>README.md</code>, which now
includes badges</li>
</ul>
</div>
<div id="major-changes-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Coil combination of GE, NIfTI-MRS, and Siemens TWIX files is now
performed using generalized least squares
(<a href="https://onlinelibrary.wiley.com/doi/10.1002/jmri.23941" target="_blank">An
et al., JMRI, 2013</a>); this approach has been shown to result in
optimal SNR and reduce spectral artifacts</li>
<li>The Gannet logo has been reverted to the original image of a
gannet</li>
</ul>
</div>
<div id="minor-changes-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added functionality for GE data in
<code>AlignSubSpectra_PreAlignRef.m</code></li>
<li>An error is presented if not enough inputs are given for any of the
Gannet modules</li>
<li>CoRegStandAlone outputs can be hidden if
<code>MRS_struct.p.hide</code> is set to <code>1</code> in
<code>CoRegStandAlone.m</code> (default is <code>0</code>)</li>
<li>If the user has no internet connection, <code>VersionCheck.m</code>
and <code>UpdateGannet.m</code> will not run</li>
<li>Updated dicm2nii to latest version (version 2022.09.15)</li>
<li>Updated mapVBVD functions to latest version
(<a href="https://github.com/pehses/mapVBVD" target="_blank">https://github.com/pehses/mapVBVD</a>)</li>
<li>Turned off warnings of iteration limits in
<code>SpectralRegistrationHERMES.m</code> and
<code>GannetFit.m</code></li>
<li>Many cosmetic changes in the code</li>
</ul>
</div>
<div id="bug-fixes-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Fixed bug in error reporting in <code>GannetFit.m</code></li>
<li>CoRegStandAlone routines now parse version numbers from the main
modules properly</li>
<li>Variable <code>filesExist</code> in <code>GannetSegment.m</code> may
not populate; it is now pre-initialized as a precaution</li>
<li>Bug fix in <code>GannetMask_SiemensRDA.m</code></li>
<li>Bug fixes for reading DICOM files</li>
</ul>
</div>
</div>
<div id="section-3" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.2.1<a href="#section-3" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2022-06-07</span></p>
<div id="minor-changes-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li><code>PhaseCorrection.m</code> now deals better with spectra that
have a non-zero baseline</li>
<li>SPM12 now outputs forward deformation field (needed for normalizing
voxel masks to MNI space)</li>
<li>Updated <code>export_fig</code> to v3.27</li>
<li><code>CoRegStandAlone.m</code> now exports a CSV file</li>
<li>Various cosmetic changes</li>
</ul>
</div>
<div id="bug-fixes-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Fixed sub-spectra alignment for GE HERCULES data</li>
<li>Fixed bug in <code>CoRegStandAlone.m</code></li>
<li>Fixed bug in <code>read_dcm_header.m</code> (thanks to Meredith
Reid)</li>
</ul>
<p><br></p>
</div>
</div>
<div id="section-4" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.2.0<a href="#section-4" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2021-07-30</span></p>
<div id="new-features-2" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features-2"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Added <code>GannetVersion.m</code>, <code>VersionCheck.m</code>, and
<code>UpdateGannet.m</code>; these new functions let users know the
version of Gannet they have, if a newer release of Gannet is available,
and will allow them to automatically update if wanted</li>
<li>Added <code>ToolboxCheck.m</code> to check for missing MATLAB
toolboxes needed to run Gannet</li>
<li>Error dialog boxes are displayed at the end of the analysis pipeline
if an error occurred (during a batch analysis, Gannet will skip to the
next dataset and continue running)</li>
<li>Users can now choose to use weighted (the default) or conventional
signal averaging in <code>GannetPreInitialise.m</code> (outlier scans
are removed when using conventional averaging, as before)</li>
<li>Added a new (optional) method for robust, weighted signal averaging:
weighted averaging by criterion function minimization (WACFM) using the
generalized Cauchy distribution as the cost function; see
doi:<a href="https://dx.doi.org/10.1016/j.bbe.2015.06.002" target="_blank">10.1016/j.bbe.2015.06.002</a>
for more details; additionally, instead of weighting difference pairs,
the subspectra of each editing subexperiment are weighted to generate
weighted subspectra, which are then subtracted; see
<code>SignalAveraging.m</code></li>
<li>Yair Altman’s
<a href="https://github.com/altmany/export_fig" target="_blank">export_fig
toolbox</a> is included as an optional toolbox that, if added to
MATLAB’s search path, Gannet will use to append all output PDFs from
each module into a single PDF (a flag must be set in
<code>GannetPreInitialise.m</code> to do this); this is very useful for
easy QA of lots of data; note that
<a href="https://www.ghostscript.com/" target="_blank">Ghostscript</a>
needs to be installed for the appending of PDFs to work (NB: macOS users
should use this
<a href="https://pages.uoregon.edu/koch/" target="_blank">version</a> or
use
<a href="https://formulae.brew.sh/formula/ghostscript" target="_blank">Homebrew</a>
to install Ghostscript)</li>
<li>Implemented use of hyperlinks in info and error messages printed in
the command window so that users can: (1) directly run a certain
function (such as <code>UpdateGannet.m</code> when
<code>VersionCheck.m</code> informs the user a new release is
available); (2) go straight to the line of code where an encountered
error can be fixed (such as errors in
<code>GannetPreInitialise.m</code>); or (3) go to a website by clicking
on the printed URL (such as to download SPM12); the relevant code has
been borrowed from export_fig</li>
<li>Added an option in <code>GannetPreInitialise.m</code> that allows
users, when using robust spectral registration, to use the averaged
pre-aligned subspectra as references for aligning the averaged
post-aligned subspectra (this may be helpful when robust spectral
registration makes the alignment of already good-quality pre-aligned
spectra worse)</li>
<li><code>PaperPlot.m</code> now allows users to plot an exemplary voxel
mask co-registered to the respective structural image</li>
<li>Added <code>GannetMask_GE_nii.m</code>; GE users can now use NIfTI
images instead of DICOMs to co-register their MRS voxels to structural
images</li>
<li>Added the ability to trim datasets</li>
<li>Extended the ability to concatenate files, including over multiple
subjects</li>
<li>Added a flag in <code>GannetPreInitialise.m</code>
(<code>MRS_struct.p.hide</code>) to prevent output figures from
displaying (useful when processing a large batch of files)</li>
</ul>
</div>
<div id="major-changes-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">Major changes<a href="#major-changes-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>The outdated manual PDF has been removed; up-to-date software
documentation will now be found online: <a
href="https://markmikkelsen.github.io/Gannet-docs/index.html"
class="uri">https://markmikkelsen.github.io/Gannet-docs/index.html</a></li>
<li>Gannet is now licensed under the BSD 3-Clause License</li>
<li>Alpha tissue correction is now performed on a by-metabolite basis
rather than fixing the intrinsic WM:GM concentration to 1:2 (alpha) for
all metabolites (assuming for now the ratio is 1:2 for GABA and Glx and
1:1 for GSH, EtOH and Lac); the alpha that is assumed is displayed in
the GannetQuantify output figure</li>
<li>Removed <code>MRS_struct.p.ON_OFF_order</code> from
<code>GannetPreInitialise.m</code>; the order of editing pulses is now
determined automatically; the relevant code has been borrowed from
Osprey (this has only been tested to a limited extent so may require
further tweaking)</li>
<li>The exception to this change is phantom data, where users will still
need to specify the order of editing pulses</li>
</ul>
</div>
<div id="minor-changes-4" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-4"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Datasets with differing number of averages can now be
batch-processed together</li>
<li>Turned off the progress bar displayed when loading Siemens TWIX data
to reduce loading time</li>
<li>Renamed some files for the sake of clarity and style; removed
obsolete <code>GannetMask.m</code></li>
<li>Signal averaging and subtraction are now done in the new function
<code>SignalAveraging.m</code></li>
<li>Various improvements to <code>RobustSpectralRegistration.m</code>
(formerly <code>Robust_Spectral_Registration.m</code>) for better
handling of data acquired using very strong water suppression</li>
<li>The assumed concentration of pure water in <code>GannetFit.m</code>
and <code>GannetFitPhantom.m</code> (PureWaterConc) has been changed
from 55 to 55.51 mol/kg; this puts it in line with the same constant
used in <code>GannetQuantify.m</code></li>
<li>Added edits from Ralph Noeske (GE Berlin) to <code>GERead.m</code>
for better handling of data when nechoes == 1; also changed the scaling
factor if nechoes > 1 (hopefully this makes water-referenced
measurements consistent across all data encoding flavors)</li>
<li>In <code>GERead.m</code> and <code>PhilipsRead_data.m</code>,
instead of using the first point in the FID for signal weighting, the
most common point that is the max in the magnitude signal across all
FIDs is now used</li>
<li>Some changes to <code>SiemensDICOMRead.m</code> and
<code>DICOMRead.m</code> for smarter handling of data files: for each
dataset, metabolite and water data files should be stored in separate
folders</li>
<li>Improved <code>ExportToCSV.m</code>; a single .csv file is now
exported for HERMES datasets; useful variables such as signal areas and
Cr fit quality metrics are now also exported</li>
<li>Rewrote <code>DiscernDataType.m</code> (formerly
<code>GannetDiscernDatatype.m</code>)</li>
<li>Minor changes and improvements to <code>PaperPlot.m</code></li>
<li>Minor changes to <code>CoRegStandAlone.m</code> functions</li>
<li>Minor changes to <code>SignalFilter.m</code></li>
<li>Simplified <code>EddyCurrentCorrection.m</code> (formerly
<code>phase_correction_fids.m</code>)</li>
<li>Set up SPM12 for batch tissue segmentation only when tissue
segmentation has not already been run and do it only once in a
batch</li>
<li>AllFramesFT (for the last loaded dataset) is now also saved in
<code>MRS_struct.spec</code></li>
<li>When saving the <code>MRS_struct</code> structure, the .mat file is
now saved using version 7.3 (for the rare case when the structure is
>= 2 GB on 64-bit computers)</li>
<li>Removed <code>MRS_struct.p.sdat</code> from
<code>GannetPreInitialise.m</code> and the corresponding code from
<code>GannetLoad.m</code> (this feature was never really used by users
afaik)</li>
<li>Improved global zero-order phasing in
<code>SpectralRegistrationHERMES.m</code></li>
<li>Many cosmetic/aesthetic changes
<ul>
<li>The module output figures now show information useful for reporting
acquisition parameters and results (in line with the
<a href="https://onlinelibrary.wiley.com/doi/10.1002/nbm.4484" target="_blank">MRSinMRS</a>
checklist)</li>
<li>Co-registered/segmented voxel masks displayed in GannetCoRegister,
GannetSegment, and GannetQuantify output figures are now shown in yellow
rather than grayscale</li>
<li>Smarter stacking of HERMES difference spectra in
<code>PlotPrePostAlign.m</code> and <code>PlotPrePostAlign2.m</code>
(formerly <code>GannetPlotPrePostAlign.m</code> and
<code>GannetPlotPrePostAlign2.m</code>)</li>
<li>The Gannet documentation website URL is printed at the bottom of
every output figure</li>
<li>Removed irrelevant messages from being printed in the command window
during the analysis pipeline, replacing them with more useful
messages</li>
<li>Minor rearranging of results text in GannetSegment and
GannetQuantify output figures</li>
<li>Slight change to the y-axis labels of the Cr frequency spectrogram
in the GannetLoad output figure</li>
<li>Better reordering of <code>MRS_struct.out</code> subfields created
in <code>GannetFit.m</code></li>
</ul></li>
</ul>
</div>
<div id="bug-fixes-4" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-4"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Frequency and phase offset estimates are now tracked correctly and
saved when running any of the spectral registration-based alignment
methods</li>
<li>Removed old debugging conditional statement in
<code>TWIXDeIdentify.m</code></li>
<li>Explicitly specify color of water frequency trace in GannetLoad
output figure as there appears to be a bug since MATLAB R2019b when
using hold to overlay plots</li>
<li>Added EtOH signal parameters to <code>GannetQuantify.m</code></li>
<li>In <code>SiemensTwixRead.m</code>, if no water reference is
provided, use the most common point that is the max in the magnitude
signal across all FIDs instead of just using the first point</li>
<li>Fixed an orientation problem in <code>GannetMask_GE.m</code></li>
<li>Removed unnecessary complex conjugate transpose during FFT of water
data in <code>GannetLoad.m</code></li>
<li>Turned off warnings about legacy number generator in
<code>RobustSpectralRegistration.m</code> (for when rng and randn are
run in <code>SignalFilter.m</code>) if they are already turned on</li>
</ul>
<p><br></p>
</div>
</div>
<div id="section-5" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.1.5<a href="#section-5" class="anchor-section"
aria-label="Anchor link to header"></a></h2>
<p><span style="color: grey;">2020-03-02</span></p>
<div id="new-features-3" class="section level3 hasAnchor">
<h3 class="hasAnchor">New features<a href="#new-features-3"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Smarter checking of incorrect settings in
<code>GannetPreInitialise.m</code> by <code>CheckTargets.m</code></li>
<li>Major changes to <code>GannetFitPhantom.m</code> to bring it more in
line with <code>GannetFit.m</code></li>
<li>Added support for CMRR MEGA-sLASER sequence in
<code>SiemensTwixRead.m</code></li>
<li>In <code>SubSpectralAlign.m</code>, if very strong water suppression
was used, use Cho instead of residual water to align subspectra of
GABA-, Lac-, and EtOH-edited datasets</li>
</ul>
</div>
<div id="minor-changes-5" class="section level3 hasAnchor">
<h3 class="hasAnchor">Minor changes<a href="#minor-changes-5"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Noise estimation in <code>CalcNoise.m</code>,
<code>Robust_Spectral_Registration.m</code>, and
<code>SignalFilter.m</code> is now performed between 8 and 10 ppm to
account for datasets that have shorter spectral widths</li>
<li>Cleaned up code in <code>GannetFit.m</code></li>
<li>Quantification of Lac now explicitly defined as Lac+MM</li>
<li>Improved functionality of <code>PaperPlot.m</code></li>
<li>In <code>SiemensTwixRead.m</code>, when a water reference is
present, coil sensitivity and phase is based on the point index that is
at the top of the echo, rather than simply fixing it to the first
point</li>
</ul>
</div>
<div id="bug-fixes-5" class="section level3 hasAnchor">
<h3 class="hasAnchor">Bug fixes<a href="#bug-fixes-5"
class="anchor-section" aria-label="Anchor link to header"></a></h3>
<ul>
<li>Minor bug fixes in CoRegStandAlone functions</li>
<li>Corrected use of random number generation in
<code>SignalFilter.m</code> when performing noise replacement to ensure
the same results are reproduced each time it is run on a dataset</li>
</ul>
<p><br></p>
</div>
</div>
<div id="section-6" class="section level2 hasAnchor">
<h2 class="hasAnchor">3.1.4<a href="#section-6" class="anchor-section"
aria-label="Anchor link to header"></a></h2>