forked from fieldtrip/fieldtrip
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathft_electrodeplacement.m
1977 lines (1750 loc) · 79.5 KB
/
ft_electrodeplacement.m
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
function [elec] = ft_electrodeplacement(cfg, varargin)
% FT_ELECTRODEPLACEMENT allows manual placement of electrodes on a MRI scan, CT scan
% or on a triangulated surface of the head. This function supports different methods.
%
% VOLUME - Navigate an orthographic display of a volume (e.g. CT or MRI scan), and
% assign an electrode label to the current crosshair location by clicking on a label
% in the eletrode list. You can undo the selection by clicking on the same label
% again. The electrode labels shown in the list can be prespecified using cfg.channel
% when calling ft_electrodeplacement. The zoom slider allows zooming in at the
% location of the crosshair. The intensity sliders allow thresholding the image's low
% and high values. The magnet feature transports the crosshair to the nearest peak
% intensity voxel, within a certain voxel radius of the selected location. The labels
% feature displays the labels of the selected electrodes within the orthoplot. The
% global feature allows toggling the view between all and near-crosshair
% markers. The scan feature allows toggling between scans when another scan
% is given as input.
%
% HEADSHAPE - Navigate a triangulated scalp (for EEG) or brain (for ECoG) surface,
% and assign an electrode location by clicking on the surface. The electrode is
% placed on the triangulation itself.
%
% 1020 - Starting from a triangulated scalp surface and the nasion, inion, left and
% right pre-auricular points, this automatically constructs and follows contours over
% the surface according to the 5% system. Electrodes are placed at certain relative
% distances along these countours. This is an extension of the 10-20 standard
% electrode placement system and includes the 20%, 10% and 5% locations. See
% "Oostenveld R, Praamstra P. The five percent electrode system for high-resolution
% EEG and ERP measurements. Clin Neurophysiol. 2001 Apr;112(4):713-9" for details.
%
% SHAFT - This is for placing electrodes along a linear sEEG shaft. The tip of the
% shaft corresponding to the first electrode, another point along the shaft, and the
% distance between the electrodes should be specified. If the shaft is not straight
% but curved, you should specify multiple (at least two) points along the shaft,
% i.e., specify cfg.shaft.along as an Nx3 array for N points along the shaft. The
% number of electrodes to be distributed along the shaft is determined from cfg.channel.
%
% GRID - This is for placing electrodes on a regular MxN ECoG grid. Each of the four
% cornerpoints of the grid must be specified, along with the dimensions of the grid.
% Following piecewise linear placement of the electrodes on the grid, you can use
% FT_ELECTRODEREALIGN with cfg.method='project' to project them to the curved brain
% surface.
%
% Use as
% [elec] = ft_electrodeplacement(cfg, mri)
% [elec] = ft_electrodeplacement(cfg, ct)
% [elec] = ft_electrodeplacement(cfg, mri, ct, ..)
% where the second and subsequent input arguments should be one or multiple
% anatomical MRIs and/or CTs, or
% [elec] = ft_electrodeplacement(cfg, headshape)
% where the input headshape should be a surface triangulation.
%
% The configuration can contain the following options
% cfg.method = string representing the method for placing the electrodes
% 'volume' interactively locate electrodes on three orthogonal slices of a volumetric MRI or CT scan
% 'headshape' interactively locate electrodes on a head surface
% '1020' automatically locate electrodes on a head surface according to the 10-20 system
% 'shaft' automatically locate electrodes along a linear sEEG shaft
% 'grid' automatically locate electrodes on a MxN ECoG grid
% cfg.figure = 'yes' or 'no', whether to open a new figure. You can also specify a figure handle from FIGURE, GCF or SUBPLOT. (default = 'yes')
% cfg.position = location and size of the figure, specified as [left bottom width height] (default is automatic)
% cfg.renderer = string, 'opengl', 'zbuffer', 'painters', see RENDERERINFO (default = 'opengl')
%
% The following options apply to the 'volume' method
% cfg.parameter = string, field in data (default = 'anatomy' if present in data)
% cfg.channel = Nx1 cell-array with selection of channels (default = {'1' '2' ...})
% cfg.elec = struct containing previously placed electrodes (this overwrites cfg.channel)
% cfg.clim = color range of the data (default = [0 1], i.e. the full range)
% cfg.magtype = string representing the 'magnet' type used for placing the electrodes
% 'peakweighted' place electrodes at weighted peak intensity voxel (default)
% 'troughweighted' place electrodes at weighted trough intensity voxel
% 'peak' place electrodes at peak intensity voxel (default)
% 'trough' place electrodes at trough intensity voxel
% 'weighted' place electrodes at center-of-mass
% cfg.magradius = number representing the radius for the cfg.magtype based search (default = 3)
%
% The following options apply to the '1020' method
% cfg.fiducial.nas = 1x3 vector with coordinates
% cfg.fiducial.ini = 1x3 vector with coordinates
% cfg.fiducial.lpa = 1x3 vector with coordinates
% cfg.fiducial.rpa = 1x3 vector with coordinates
% cfg.feedback = string, can be 'yes' or 'no' for detailled feedback (default = 'yes')
%
% The following options apply to the 'shaft' method
% cfg.shaft.tip = 1x3 position of the electrode at the tip of the shaft
% cfg.shaft.along = 1x3 or Nx3 positions along the shaft
% cfg.shaft.distance = scalar, distance between electrodes
%
% The following options apply to the 'grid' method
% cfg.grid.corner1 = 1x3 position of the upper left corner point
% cfg.grid.corner2 = 1x3 position of the upper right corner point
% cfg.grid.corner3 = 1x3 position of the lower left corner point
% cfg.grid.corner4 = 1x3 position of the lower right corner point
%
% In the interactive 'headshape' and 'volume' methods you can click once on an
% already assigned electrode to jump to that electrode position and you can click
% twice to remove the assigned electrode position.
%
% See also FT_ELECTRODEREALIGN, FT_VOLUMEREALIGN, FT_VOLUMESEGMENT, FT_PREPARE_MESH
% Copyright (C) 2015-2019, Arjen Stolk, Sandon Griffin & Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar mri
ft_preamble provenance mri
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% ensure that old and unsupported options are not being relied on by the end-user's script
% see http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2837
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'forbidden', {'channels'}); % prevent accidental typos, see issue 1729
cfg = ft_checkconfig(cfg, 'renamed', {'viewdim', 'axisratio'});
cfg = ft_checkconfig(cfg, 'renamedval', {'method', 'mri', 'volume'});
cfg = ft_checkconfig(cfg, 'renamed', {'newfigure', 'figure'});
% set the defaults
cfg.method = ft_getopt(cfg, 'method', []); % volume, headshape, 1020, shaft
cfg.feedback = ft_getopt(cfg, 'feedback', 'yes');
cfg.parameter = ft_getopt(cfg, 'parameter', 'anatomy');
cfg.channel = ft_getopt(cfg, 'channel', []); % default will be determined further down {'1', '2', ...}
cfg.elec = ft_getopt(cfg, 'elec', []); % use previously placed electrodes
cfg.flip = ft_getopt(cfg, 'flip', []); % the default is set below
cfg.renderer = ft_getopt(cfg, 'renderer', 'opengl');
% view options
cfg.clim = ft_getopt(cfg, 'clim', [0 1]); % initial volume intensity limit voxels
cfg.markerdist = ft_getopt(cfg, 'markerdist', 5); % marker-slice distance view when ~global
% magnet options
cfg.magtype = ft_getopt(cfg, 'magtype', 'peakweighted'); % detect weighted peaks or troughs
cfg.magradius = ft_getopt(cfg, 'magradius', 3); % specify the physical unit radius
cfg.voxelratio = ft_getopt(cfg, 'voxelratio', 'data'); % display size of the voxel, 'data' or 'square'
cfg.axisratio = ft_getopt(cfg, 'axisratio', 'data'); % size of the axes of the three orthoplots, 'square', 'voxel', or 'data'
if isempty(cfg.method) && ~isempty(varargin)
% the default determines on the input data
switch ft_datatype(varargin{1})
case 'volume'
cfg.method = 'volume';
case 'mesh'
cfg.method = 'headshape';
case 'source+mesh'
cfg.method = 'headshape';
end
end
if isempty(cfg.flip)
if strcmp(cfg.method, 'volume')
cfg.flip = 'yes';
else
cfg.flip = 'no';
end
end
% check if the input data is valid for this function
switch cfg.method
case 'volume'
for v = 1:numel(varargin)
mri{v} = ft_checkdata(varargin{v}, 'datatype', 'volume', 'feedback', 'yes', 'hascoordsys', 'yes', 'hasunit', 'yes');
end
case {'headshape', '1020'}
headshape = fixpos(varargin{1});
headshape = ft_checkdata(headshape, 'hascoordsys', 'yes', 'hasunit', 'yes');
end
if strcmp(cfg.flip, 'yes')
for v = 1:numel(varargin)
% align the anatomical volume approximately to coordinate system, this puts it upright
origmethod = cfg.method;
tmpcfg = [];
tmpcfg.method = 'flip';
tmpcfg.trackcallinfo = 'no';
tmpcfg.showcallinfo = 'no';
mri{v} = ft_volumereslice(tmpcfg, mri{v});
[cfg, mri] = rollback_provenance(cfg, mri);
cfg.method = origmethod;
end
end
% setup electrode labels if possible
chanlabel = {};
chanstring = {};
markerlab = {};
markerpos = {};
if ~isempty(cfg.elec) % re-use previously placed (cfg.elec) electrodes
for e = 1:numel(cfg.elec.label)
chanlabel{end+1,1} = cfg.elec.label{e};
chanstring{end+1} = ['<HTML><FONT color="black">' cfg.elec.label{e} '</FONT></HTML>']; % hmtl'ize
markerlab{end+1,1} = cfg.elec.label{e};
markerpos{end+1,1} = cfg.elec.elecpos(e,:);
end
end
if ~isempty(cfg.channel) % use prespecified (cfg.channel) electrode labels
for c = 1:numel(cfg.channel)
if ~ismember(cfg.channel{c}, chanlabel) % avoid overlap between cfg.channel and elec.label
chanlabel{end+1,1} = cfg.channel{c};
chanstring{end+1} = ['<HTML><FONT color="silver">' cfg.channel{c} '</FONT></HTML>']; % hmtl'ize
markerlab{end+1,1} = [];
markerpos{end+1,1} = zeros(0,3);
end
end
end
if isempty(cfg.elec) && isempty(cfg.channel) % create electrode labels on-the-fly
for c = 1:300
chanlabel{end+1,1} = sprintf('%d', c);
chanstring{end+1} = ['<HTML><FONT color="silver">' sprintf('%d', c) '</FONT></HTML>']; % hmtl'ize
markerlab{end+1,1} = {};
markerpos{end+1,1} = zeros(0,3);
end
end
% this is where the different methods are implemented
switch cfg.method
case 'volume'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this is an interactive method, start building the figure
h = open_figure(keepfields(cfg, {'figure', 'position', 'visible', 'renderer', 'figurename', 'title'}));
set(h, 'Name', mfilename);
set(h, 'Units', 'normalized');
set(h, 'Color', [1 1 1]);
set(h, 'MenuBar', 'none');
set(h, 'windowbuttondownfcn', @cb_buttonpress);
set(h, 'windowbuttonupfcn', @cb_buttonrelease);
set(h, 'windowkeypressfcn', @cb_keyboard);
set(h, 'CloseRequestFcn', @cb_quit);
% volume-dependent axis settings
for v = 1:numel(mri)
if strcmp(cfg.axisratio, 'voxel')
% determine the number of voxels to be plotted along each axis
axlen1 = mri{v}.dim(1);
axlen2 = mri{v}.dim(2);
axlen3 = mri{v}.dim(3);
elseif strcmp(cfg.axisratio, 'data')
% determine the length of the edges along each axis
[cp_voxel, cp_head] = cornerpoints(mri{v}.dim, mri{v}.transform);
axlen1 = norm(cp_head(2,:)-cp_head(1,:));
axlen2 = norm(cp_head(4,:)-cp_head(1,:));
axlen3 = norm(cp_head(5,:)-cp_head(1,:));
elseif strcmp(cfg.axisratio, 'square')
% the length of the axes should be equal
axlen1 = 1;
axlen2 = 1;
axlen3 = 1;
end
% this is the size reserved for subplot h1, h2 and h3
h1size(1) = 0.92*axlen1/(axlen1 + axlen2); % x
h1size(2) = 0.92*axlen3/(axlen2 + axlen3); % z
h2size(1) = 0.92*axlen2/(axlen1 + axlen2); % y
h2size(2) = 0.92*axlen3/(axlen2 + axlen3); % z
h3size(1) = 0.92*axlen1/(axlen1 + axlen2); % x
h3size(2) = 0.92*axlen2/(axlen2 + axlen3); % y
% axis handles will hold the anatomical functional if present, along with labels etc.
h1 = axes('position', [0.02 0.02+0.04+h3size(2) h1size(1) h1size(2)]); % x z
h2 = axes('position', [0.02+0.04+h1size(1) 0.02+0.04+h3size(2) h2size(1) h2size(2)]); % y z
h3 = axes('position', [0.02 0.02 h3size(1) h3size(2)]); % x y
set(h1, 'Tag', 'ik', 'Visible', 'off', 'XAxisLocation', 'top'); axis(h1, 'equal');
set(h2, 'Tag', 'jk', 'Visible', 'off', 'YAxisLocation', 'right'); axis(h2, 'equal'); % after rotating in ft_plot_ortho this becomes top
set(h3, 'Tag', 'ij', 'Visible', 'off'); axis(h3, 'equal');
if strcmp(cfg.voxelratio, 'square')
voxlen1 = 1;
voxlen2 = 1;
voxlen3 = 1;
elseif strcmp(cfg.voxelratio, 'data')
% the size of the voxel is scaled with the data
[cp_voxel, cp_head] = cornerpoints(mri{v}.dim, mri{v}.transform);
voxlen1 = norm(cp_head(2,:)-cp_head(1,:))/norm(cp_voxel(2,:)-cp_voxel(1,:));
voxlen2 = norm(cp_head(4,:)-cp_head(1,:))/norm(cp_voxel(4,:)-cp_voxel(1,:));
voxlen3 = norm(cp_head(5,:)-cp_head(1,:))/norm(cp_voxel(5,:)-cp_voxel(1,:));
end
%set(h1, 'DataAspectRatio', 1./[voxlen1 voxlen2 voxlen3]); % FIXME: this no longer works when using mri.transform with ft_plot_ortho (instead of eye(4));
%set(h2, 'DataAspectRatio', 1./[voxlen1 voxlen2 voxlen3]);
%set(h3, 'DataAspectRatio', 1./[voxlen1 voxlen2 voxlen3]);
mri{v}.axes = [h1 h2 h3];
mri{v}.h1size = h1size;
mri{v}.h2size = h2size;
mri{v}.h3size = h3size;
mri{v}.clim = cfg.clim;
mri{v}.slim = [.9 1]; % 90% - maximum
dat = double(mri{v}.(cfg.parameter));
dmin = min(dat(:));
dmax = max(dat(:));
mri{v}.dat = (dat-dmin)./(dmax-dmin); % range between 0 and 1
clear dat dmin dmax
end
% intensity range sliders
h45text = uicontrol('Style', 'text',...
'String', 'Intensity',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.02 mri{1}.h3size(2)-0.02 mri{1}.h1size(1)/4 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');
h4 = uicontrol('Style', 'slider', ...
'Parent', h, ...
'Min', 0, 'Max', 1, ...
'Value', cfg.clim(1), ...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.03 0.10+mri{1}.h3size(2)/3 0.05 mri{1}.h3size(2)/2-0.05], ...
'Callback', @cb_minslider);
h5 = uicontrol('Style', 'slider', ...
'Parent', h, ...
'Min', 0, 'Max', 1, ...
'Value', cfg.clim(2), ...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)+0.02 0.10+mri{1}.h3size(2)/3 0.05 mri{1}.h3size(2)/2-0.05], ...
'Callback', @cb_maxslider);
% java intensity range slider (dual-knob slider): the java component gives issues when wanting to
% access the opt structure
% [jRangeSlider] = com.jidesoft.swing.RangeSlider(0,1,cfg.clim(1),cfg.clim(2)); % min,max,low,high
% [jRangeSlider, h4] = javacomponent(jRangeSlider, [], h);
% set(h4, 'Units', 'normalized', 'Position', [0.05+h1size(1) 0.07 0.07 h3size(2)], 'Parent', h);
% set(jRangeSlider, 'Orientation', 1, 'PaintTicks', true, 'PaintLabels', true, ...
% 'Background', java.awt.Color.white, 'StateChangedCallback', @cb_intensityslider);
% electrode listbox
h6 = uicontrol('Style', 'listbox', ...
'Parent', h, ...
'Value', [], 'Min', 0, 'Max', numel(chanstring), ...
'Units', 'normalized', ...
'FontSize', 12, ...
'Position', [mri{1}.h1size(1)+0.07 0.02 mri{1}.h2size(1)/2.5 mri{1}.h3size(2)], ...
'Callback', @cb_eleclistbox, ...
'String', chanstring);
% switches / radio buttons
h7text = uicontrol('Style', 'text',...
'String', 'Magnet',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.047 0.18 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');
h7 = uicontrol('Style', 'popupmenu',...
'Parent', h, ...
'Value', 4, ... % corresponding to magradius = 3 (see String)
'String', {'0', '1', '2', '3', '4', '5', '6', '7', '8', '9'}, ...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.103 0.18 mri{1}.h1size(1)/4.25 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_magnetbutton);
radii = get(h7, 'String');
if ~ismember(num2str(cfg.magradius), radii) % add user-specified radius to the list
set(h7, 'String', [radii(:); num2str(cfg.magradius)]);
set(h7, 'Value', numel(radii)+1);
end
h8 = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'Labels',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.14 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_labelsbutton);
h9 = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'Global',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.10 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_globalbutton);
hscatter = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'Scatter',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.06 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_scatterbutton);
hscan = uicontrol('Style', 'checkbox',...
'Parent', h, ...
'Value', 0, ...
'String', 'CT/MRI',...
'Units', 'normalized', ...
'Position', [2*mri{1}.h1size(1)-0.05 0.02 mri{1}.h1size(1)/3 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Visible', 'off', ...
'Callback', @cb_scanbutton);
if numel(mri)>1; set(hscan, 'Visible', 'on'); end % only when two scans are given as input
% zoom slider
h10text = uicontrol('Style', 'text',...
'String', 'Zoom',...
'Units', 'normalized', ...
'Position', [1.8*mri{1}.h1size(1)-0.04 mri{1}.h3size(2)-0.02 mri{1}.h1size(1)/4 0.04],...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on');
h10 = uicontrol('Style', 'slider', ...
'Parent', h, ...
'Min', 0, 'Max', 0.9, ...
'Value', 0, ...
'Units', 'normalized', ...
'Position', [1.8*mri{1}.h1size(1)-0.03 0.10+mri{1}.h3size(2)/3 0.05 mri{1}.h3size(2)/2-0.05], ...
'SliderStep', [.1 .1], ...
'Callback', @cb_zoomslider);
% create structure to be passed to gui
opt = [];
opt.method = 'volume'; % this is to distinguish between volume and headshape in the callbacks
opt.label = chanlabel;
opt.handlesaxes = [mri{1}.axes(1) mri{1}.axes(2) mri{1}.axes(3) h4 h5 h6 h7 h8 h9 h10 hscatter hscan];
opt.mainfig = h;
opt.quit = false;
opt.update = [1 1 1];
opt.init = true;
opt.tag = 'ik';
opt.ana = mri{1}.dat; % the plotted anatomy
opt.mri = mri;
opt.currmri = 1;
opt.showcrosshair = true;
opt.pos = [0 0 0]; % middle of the scan, head coordinates
opt.showsurface = true;
opt.showlabels = false;
opt.showcolors = false;
opt.magnet = get(h7, 'Value');
opt.magradius = cfg.magradius;
opt.magtype = cfg.magtype;
opt.showmarkers = true;
opt.global = get(h9, 'Value'); % show all markers in the current slices
opt.scatter = get(hscatter, 'Value'); % additional scatterplot
opt.scan = get(hscan, 'Value'); % switch scans
opt.slim = [.9 1]; % 90% - maximum
opt.markerlab = markerlab;
opt.markerpos = markerpos;
opt.markerdist = cfg.markerdist; % hidden option
opt.clim = cfg.clim;
opt.zoom = 0;
setappdata(h, 'opt', opt);
cb_redraw(h);
cb_help(h);
while(opt.quit==0)
uiwait(h);
opt = getappdata(h, 'opt');
end
delete(h);
% collect the results
elec = keepfields(mri{1}, {'unit', 'coordsys'});
elec.label = {};
elec.elecpos = [];
for i=1:length(opt.markerlab)
if ~isempty(opt.markerlab{i,1})
elec.label = [elec.label; opt.markerlab{i,1}];
elec.elecpos = [elec.elecpos; opt.markerpos{i,1}];
end
end
elec.chanpos = elec.elecpos;
elec.tra = eye(size(elec.elecpos,1));
case 'headshape'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this is an interactive method, start building the figure
h = open_figure(keepfields(cfg, {'figure', 'position', 'visible', 'renderer', 'figurename', 'title'}));
set(h, 'Name', mfilename);
set(h, 'Units', 'normalized');
set(h, 'Color', [1 1 1]);
set(h, 'windowbuttondownfcn', @cb_buttonpress);
set(h, 'windowbuttonupfcn', @cb_buttonrelease);
set(h, 'windowkeypressfcn', @cb_keyboard);
set(h, 'CloseRequestFcn', @cb_quit);
% electrode listbox
h1 = uicontrol('Style', 'listbox', ...
'Parent', h, ...
'Value', [], 'Min', 0, 'Max', numel(chanstring), ...
'Units', 'normalized', ...
'FontSize', 12, ...
'Position', [.8 0.001 .2 .5], ...
'Callback', @cb_eleclistbox, ...
'String', chanstring);
h7 = uicontrol('Style', 'checkbox', ...
'Parent', h, ...
'Value', 1, ...
'String', 'Surface', ...
'Units', 'normalized', ...
'Position', [.8 0.65 .2 .05], ...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_surfacebutton);
h8 = uicontrol('Style', 'checkbox', ...
'Parent', h, ...
'Value', 0, ...
'String', 'Labels', ...
'Units', 'normalized', ...
'Position', [.8 0.6 .2 .05], ...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_labelsbutton);
if isfield(headshape, 'color')
h9 = uicontrol('Style', 'checkbox', ...
'Parent', h, ...
'Value', 1, ...
'String', 'Colors', ...
'Units', 'normalized', ...
'Position', [.8 0.55 .2 .05], ...
'BackgroundColor', [1 1 1], ...
'HandleVisibility', 'on', ...
'Callback', @cb_colorsbutton);
end
% create structure to be passed to gui
opt = [];
opt.method = 'headshape'; % this is to distinguish between volume and headshape in the callbacks
opt.headshape = headshape;
opt.label = chanlabel;
opt.handlesaxes = [h1 h8];
opt.mainfig = h;
opt.quit = false;
opt.init = true;
opt.pos = [0 0 0]; % middle of the scan, head coordinates (FIXME: this might mess up vertex finding, being an anchor)
opt.showcrosshair = true;
opt.showsurface = true;
opt.showlabels = false;
opt.showcolors = true;
opt.showmarkers = true;
opt.markerlab = markerlab;
opt.markerpos = markerpos;
opt.markerdist = cfg.markerdist; % hidden option
setappdata(h, 'opt', opt);
cb_help(h);
cb_headshaperedraw(h);
view([90, 0]);
while(opt.quit==0)
uiwait(h);
opt = getappdata(h, 'opt');
end
delete(h);
% collect the results
elec = keepfields(headshape, {'unit', 'coordsys'});
elec.label = {};
elec.elecpos = [];
for i=1:length(opt.markerlab)
if ~isempty(opt.markerlab{i,1})
elec.label = [elec.label; opt.markerlab{i,1}];
elec.elecpos = [elec.elecpos; opt.markerpos{i,1}];
end
end
elec.chanpos = elec.elecpos;
elec.tra = eye(size(elec.elecpos,1));
case '1020'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this is an automatic method without figure
% the placement procedure fails if the fiducials coincide with vertices
dist = @(x, y) sqrt(sum(bsxfun(@minus, x, y).^2,2));
tolerance = 0.1 * ft_scalingfactor('mm', headshape.unit); % 0.1 mm
nas = cfg.fiducial.nas;
ini = cfg.fiducial.ini;
lpa = cfg.fiducial.lpa;
rpa = cfg.fiducial.rpa;
if any(dist(headshape.pos, nas)<tolerance)
ft_warning('Nasion coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
nas = nas + tolerance*randn(1,3);
end
if any(dist(headshape.pos, ini)<tolerance)
ft_warning('Inion coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
ini = ini + tolerance*randn(1,3);
end
if any(dist(headshape.pos, lpa)<tolerance)
ft_warning('LPA coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
lpa = lpa + tolerance*randn(1,3);
end
if any(dist(headshape.pos, rpa)<tolerance)
ft_warning('RPA coincides with headshape vertex, addding random displacement of about %f %s', tolerance, headshape.unit);
rpa = rpa + tolerance*randn(1,3);
end
% place the electrodes automatically according to the fiducials
[pos, lab] = elec1020_locate(headshape.pos, headshape.tri, nas, ini, lpa, rpa, istrue(cfg.feedback));
% construct the output
elec = keepfields(headshape, {'unit', 'coordsys'});
elec.elecpos = pos;
elec.label = lab(:);
case 'shaft'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this is an automatic method without figure
if size(cfg.shaft.along,1)==1
% two points are specified, use a simple linear method
pos = cfg.shaft.tip;
ori = cfg.shaft.along - cfg.shaft.tip;
ori = ori/norm(ori);
elec = [];
elec.label = cfg.channel;
for i=1:numel(elec.label)
elec.elecpos(i,:) = pos + (i-1) * ori * cfg.shaft.distance;
end
else
% more than two points are specified, use a spline
pos = [
cfg.shaft.tip
cfg.shaft.along
];
dist = sqrt(sum(diff(pos,1,1).^2, 2)); % distance between subsequent positions
dist = [0; cumsum(dist)]; % cumulative distance from the tip
cv = csapi(dist', pos'); % spline that goes through all positions
elec = [];
elec.label = cfg.channel;
for i=1:numel(elec.label)
dist = (i-1) * cfg.shaft.distance;
elec.elecpos(i,:) = cfg.shaft.tip + fnval(cv, dist)';
end
end
case 'grid'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this is an automatic method without figure
% The four cornerpoints specified by the user will not exactly be a rectangle,
% but will have in plane distortion and out-of-plane twist.
% Each cornerpoint with the two edges to its direct neighbours describes a parallellogram.
% We compute the position of each electrode according to this parallellogram
% and then compute the weighted average based on distance to the cornerpoints.
% The cornerpoints are specified like this
%
% 1 2
% 3 4
% parallellogram starting in corner 1
dir12 = cfg.grid.corner2-cfg.grid.corner1; dir12 = dir12/norm(dir12);
dir13 = cfg.grid.corner3-cfg.grid.corner1; dir13 = dir13/norm(dir13);
% parallellogram starting in corner 2
dir21 = cfg.grid.corner1-cfg.grid.corner2; dir21 = dir21/norm(dir21);
dir24 = cfg.grid.corner4-cfg.grid.corner2; dir24 = dir24/norm(dir24);
% parallellogram starting in corner 3
dir31 = cfg.grid.corner1-cfg.grid.corner3; dir31 = dir31/norm(dir31);
dir34 = cfg.grid.corner4-cfg.grid.corner3; dir34 = dir34/norm(dir34);
% parallellogram starting in corner 4
dir42 = cfg.grid.corner2-cfg.grid.corner4; dir42 = dir42/norm(dir42);
dir43 = cfg.grid.corner3-cfg.grid.corner4; dir43 = dir43/norm(dir43);
% assuming a 3x4 grid, the electrodes will be placed like this
%
% 1 2 3 4
% 5 6 7 8
% 9 10 11 12
% specify the number of electrodes in the vertical and horizontal direction
nv = cfg.grid.dim(1);
nh = cfg.grid.dim(2);
% determine the inter-electrode distance in the vertical and horizontal direction
dv = (norm(cfg.grid.corner3-cfg.grid.corner1)/(nv-1) + norm(cfg.grid.corner4-cfg.grid.corner2)/(nv-1))/2;
dh = (norm(cfg.grid.corner2-cfg.grid.corner1)/(nh-1) + norm(cfg.grid.corner4-cfg.grid.corner3)/(nh-1))/2;
ft_notice('electrode spacing along 1st dimension is %f', dv);
ft_notice('electrode spacing along 2nd dimension is %f', dh);
% scale the
dir12 = dir12*dh;
dir13 = dir13*dv;
dir21 = dir21*dh;
dir24 = dir24*dv;
dir31 = dir31*dv;
dir34 = dir34*dh;
dir42 = dir42*dv;
dir43 = dir43*dh;
if isempty(cfg.channel)
ft_notice('using automatic channel labels');
cfg.channel = arrayfun(@num2str, 1:(nh*nv), 'UniformOutput', false);
else
assert(numel(cfg.channel)==nh*nv, 'mismatch between cfg.grid.dim and cfg.channel');
end
pos1 = nan(nh*nv,3);
pos2 = nan(nh*nv,3);
pos3 = nan(nh*nv,3);
pos4 = nan(nh*nv,3);
% determine the position of each electrode according to each parallellogram
k = 1;
for i=1:nv
for j=1:nh
pos1(k,:) = ( i-1)*dir13 + ( j-1)*dir12 + cfg.grid.corner1;
pos2(k,:) = ( i-1)*dir24 + (nh-j)*dir21 + cfg.grid.corner2;
pos3(k,:) = (nv-i)*dir31 + ( j-1)*dir34 + cfg.grid.corner3;
pos4(k,:) = (nv-i)*dir42 + (nh-j)*dir43 + cfg.grid.corner4;
k = k+1;
end % horizontal
end % vertical
d1 = nan(nh*nv,1);
d2 = nan(nh*nv,1);
d3 = nan(nh*nv,1);
d4 = nan(nh*nv,1);
% determine the schematic distance (i.e. counted in steps) to each corner
k = 1;
for i=1:nv
for j=1:nh
d1(k) = norm([( i-1)*dv ( j-1)*dh]);
d2(k) = norm([( i-1)*dv (nh-j)*dh]);
d3(k) = norm([(nv-i)*dv ( j-1)*dh]);
d4(k) = norm([(nv-i)*dv (nh-j)*dh]);
k = k+1;
end % horizontal
end % vertical
% the weight is relative to the range, which is 0.5 times the dimagonal distance
range = sqrt(((nv-1)*dv)^2 + ((nh-1)*dh)^2) / 2;
% compute the weights from the distance
d1 = 10.^(-d1/range);
d2 = 10.^(-d2/range);
d3 = 10.^(-d3/range);
d4 = 10.^(-d4/range);
% normalize the weights
dd = (d1 + d2 + d3 + d4);
d1 = d1 ./ dd;
d2 = d2 ./ dd;
d3 = d3 ./ dd;
d4 = d4 ./ dd;
% compute the weighted position
elec = [];
elec.label = cfg.channel;
elec.elecpos = [d1 d1 d1].*pos1 + [d2 d2 d2].*pos2 + [d3 d3 d3].*pos3 + [d4 d4 d4].*pos4;
otherwise
ft_error('unsupported method ''%s''', cfg.method);
end % switch method
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous mri
ft_postamble provenance elec
ft_postamble history elec
ft_postamble savevar elec
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function cb_help(h, eventdata)
h = getparent(h);
opt = getappdata(h, 'opt');
switch opt.method
case 'volume'
disp('==================================================================================');
disp('0. Press "h" to show this help');
disp('1. Options for viewing:');
disp(' a. use the left mouse button to navigate in the image, or');
disp(' b. use the arrow keys to increase or decrease the slice number by one');
disp('2. Options for electrode placement:');
disp(' a. click an electrode label in the list to assign it to the crosshair location, or');
disp(' b. doubleclick a previously assigned electrode label to remove its marker');
disp('3. Press "q" on the keyboard or close the window when you are done');
disp('4. See Stolk, Griffin et al. Nature Protocols 2018 for further electrode processing options');
case 'headshape'
disp('==================================================================================');
disp('0. Press "h" to show this help');
disp('1. Options for electrode placement:');
disp(' a. Use the mouse to click on the desired position for an electrode');
disp(' b. Click on the corresponding electrode label');
disp('2. Press "v" to update the light position');
disp('3. Press "q" or close the window when you are done');
end % switch
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function cb_redraw(h, eventdata)
h = getparent(h);
opt = getappdata(h, 'opt');
% determine current axes
set(0, 'CurrentFigure', opt.mainfig);
curr_ax = get(h, 'currentaxes');
tag = get(curr_ax, 'tag');
h1 = opt.handlesaxes(1);
h2 = opt.handlesaxes(2);
h3 = opt.handlesaxes(3);
if opt.init
delete(findobj(opt.mainfig, 'Type', 'Surface')); % get rid of old orthos (to facilitate switching scans)
ft_plot_ortho(opt.ana, 'transform', opt.mri{opt.currmri}.transform, 'coordsys', opt.mri{opt.currmri}.coordsys, 'location', opt.pos, 'style', 'subplot', 'parents', [h1 h2 h3], 'update', opt.update, 'doscale', false, 'clim', opt.clim, 'unit', opt.mri{opt.currmri}.unit);
opt.anahandles = findobj(opt.mainfig, 'Type', 'Surface')';
parenttag = get(opt.anahandles, 'parent');
parenttag{1} = get(parenttag{1}, 'tag');
parenttag{2} = get(parenttag{2}, 'tag');
parenttag{3} = get(parenttag{3}, 'tag');
[i1,i2,i3] = intersect(parenttag, {'ik';'jk';'ij'});
opt.anahandles = opt.anahandles(i3(i2)); % seems like swapping the order
opt.anahandles = opt.anahandles(:)';
set(opt.anahandles, 'tag', 'ana');
% for zooming purposes
opt.axis = [opt.handlesaxes(1).XLim opt.handlesaxes(1).YLim opt.handlesaxes(1).ZLim];
opt.redrawmarkers = true;
opt.reinit = false; % do not redraw orthoplots
elseif opt.reinit
ft_plot_ortho(opt.ana, 'transform', opt.mri{opt.currmri}.transform, 'coordsys', opt.mri{opt.currmri}.coordsys, 'location', opt.pos, 'style', 'subplot', 'surfhandle', opt.anahandles, 'update', opt.update, 'doscale', false, 'clim', opt.clim, 'unit', opt.mri{opt.currmri}.unit);
fprintf('==================================================================================\n');
lab = 'crosshair';
switch opt.mri{opt.currmri}.unit
case 'mm'
fprintf('%10s at [%.1f %.1f %.1f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
case 'cm'
fprintf('%10s at [%.2f %.2f %.2f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
case 'm'
fprintf('%10s at [%.4f %.4f %.4f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
otherwise
fprintf('%10s at [%f %f %f] %s\n', lab, opt.pos, opt.mri{opt.currmri}.unit);
end
opt.reinit = false; % do not redraw orthoplots
end
% zoom
xi = opt.pos(1);
yi = opt.pos(2);
zi = opt.pos(3);
xloadj = ((xi-opt.axis(1))-(xi-opt.axis(1))*opt.zoom);
xhiadj = ((opt.axis(2)-xi)-(opt.axis(2)-xi)*opt.zoom);
yloadj = ((yi-opt.axis(3))-(yi-opt.axis(3))*opt.zoom);
yhiadj = ((opt.axis(4)-yi)-(opt.axis(4)-yi)*opt.zoom);
zloadj = ((zi-opt.axis(5))-(zi-opt.axis(5))*opt.zoom);
zhiadj = ((opt.axis(6)-zi)-(opt.axis(6)-zi)*opt.zoom);
axis(h1, [xi-xloadj xi+xhiadj yi-yloadj yi+yhiadj zi-zloadj zi+zhiadj]);
axis(h2, [xi-xloadj xi+xhiadj yi-yloadj yi+yhiadj zi-zloadj zi+zhiadj]);
axis(h3, [xi-xloadj xi+xhiadj yi-yloadj yi+yhiadj]);
if opt.zoom>0
% the coordsys labels fall outside the subplots when zoomed in
delete(findall(h, 'Type', 'text', 'Tag', 'coordsys_label_100'));
delete(findall(h, 'Type', 'text', 'Tag', 'coordsys_label_010'));
delete(findall(h, 'Type', 'text', 'Tag', 'coordsys_label_001'));
end
if opt.init
% draw the crosshairs for the first time
delete(findobj(opt.mainfig, 'Type', 'Line')); % get rid of old crosshairs (to facilitate switching scans)
hch1 = ft_plot_crosshair([xi yi-yloadj zi], 'parent', h1, 'color', 'yellow'); % was [xi 1 zi], now corrected for zoom
hch2 = ft_plot_crosshair([xi+xhiadj yi zi], 'parent', h2, 'color', 'yellow'); % was [opt.dim(1) yi zi], now corrected for zoom
hch3 = ft_plot_crosshair([xi yi zi], 'parent', h3, 'color', 'yellow'); % was [xi yi opt.dim(3)], now corrected for zoom
opt.handlescross = [hch1(:)';hch2(:)';hch3(:)'];
else
% update the existing crosshairs, don't change the handles
ft_plot_crosshair([xi yi-yloadj zi], 'handle', opt.handlescross(1, :));
ft_plot_crosshair([xi+xhiadj yi zi], 'handle', opt.handlescross(2, :));
ft_plot_crosshair([xi yi zi], 'handle', opt.handlescross(3, :));
end
if opt.showcrosshair
set(opt.handlescross, 'Visible', 'on');
else
set(opt.handlescross, 'Visible', 'off');
end
% draw markers
if opt.showmarkers && opt.redrawmarkers
delete(findobj(opt.mainfig, 'Tag', 'marker')); % remove previous markers
delete(findobj(opt.mainfig, 'Tag', 'label')); % remove previous labels
idx = find(~cellfun(@isempty,opt.markerlab)); % non-empty markers
if ~isempty(idx)
for i=1:numel(idx)
markerlab_sel{i,1} = opt.markerlab{idx(i),1};
markerpos_sel(i,:) = opt.markerpos{idx(i),1};
end
tmp1 = markerpos_sel(:,1);
tmp2 = markerpos_sel(:,2);
tmp3 = markerpos_sel(:,3);
subplot(opt.handlesaxes(1));
if ~opt.global % filter markers distant to the current slice (N units and further)
posj_idx = find( abs(tmp2 - repmat(yi,size(tmp2))) < opt.markerdist);
posi = tmp1(posj_idx);
posj = tmp2(posj_idx);
posk = tmp3(posj_idx);
else % plot all markers on the current slice
posj_idx = 1:numel(tmp1);
posi = tmp1;
posj = tmp2;
posk = tmp3;
end
if ~isempty(posi)
hold on
plot3(posi, repmat(yi-yloadj,size(posj)), posk, 'Marker', '+', 'LineStyle', 'none', 'Color', 'r', 'Tag', 'marker'); % [xi yi-yloadj zi]
if opt.showlabels
for i=1:numel(posj_idx)
text(posi(i), yi-yloadj, posk(i), markerlab_sel{posj_idx(i),1}, 'Color', [1 .5 0], 'Clipping', 'on', 'Tag', 'label');
end
end
hold off
end
subplot(opt.handlesaxes(2));
if ~opt.global % filter markers distant to the current slice (N units and further)
posi_idx = find( abs(tmp1 - repmat(xi,size(tmp1))) < opt.markerdist);
posi = tmp1(posi_idx);
posj = tmp2(posi_idx);
posk = tmp3(posi_idx);
else % plot all markers on the current slice
posi_idx = 1:numel(tmp1);
posi = tmp1;
posj = tmp2;
posk = tmp3;
end
if ~isempty(posj)
hold on
plot3(repmat(xi+xhiadj,size(posi)), posj, posk, 'marker', '+', 'linestyle', 'none', 'color', 'r'); % [xi+xhiadj yi zi]
if opt.showlabels
for i=1:numel(posi_idx)
text(posi(i)+xhiadj, posj(i), posk(i), markerlab_sel{posi_idx(i),1}, 'color', [1 .5 0], 'clipping', 'on');
end
end
hold off
end
subplot(opt.handlesaxes(3));
if ~opt.global % filter markers distant to the current slice (N units and further)
posk_idx = find( abs(tmp3 - repmat(zi,size(tmp3))) < opt.markerdist);
posi = tmp1(posk_idx);
posj = tmp2(posk_idx);
posk = tmp3(posk_idx);
else % plot all markers on the current slice