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
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title>SNAP Tutorial. Section 6.</title>
<meta content="text/html; charset=iso-8859-1"
http-equiv="Content-Type">
</head>
<body>
<h2>Section 6. Automatic Segmentation using Region Competition Snakes</h2>
<p>This section gives step by step instructions on segmenting an image
using the region competition snake (in last section's terminology,
snake evolution that uses the region feature image). This section
assumes that you are working with the image <strong>MRIcrop-orig.gipl</strong>,
as recommended in <a href="TutorialSectionLoadingImages.html#Download">Section
2, Step 1</a>. We will segment the caudate nucleus and the ventricles
in this image. This section also assumes that you are using the label
file <strong>MRIcrop-seg.label</strong>. </p>
<p>You can, however, follow the general directions of this section
using a different image, but you will have to use your own judgement in
selecting various parameters.</p>
<hr>
<h3><a name="discard"></a>Step 1. Discard the Previous Segmentation.</h3>
<p>In <a href="TutorialSectionManualSegmentation.html">Section 4</a>,
we have created a manual segmentation. In order to perform the
segmentation automatically, we will discard the manual segmetnation.
This involves reloading the greyscale image. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select <strong>File | Load Data | Greyscale Image</strong>.</p>
<p>Use the <strong>History</strong> button to select the image
loaded most recently.</p>
<p>Step through the rest of the wizard, as descibed in <a
href="TutorialSectionLoadingImages.html#Orientation">Section 2</a>. </p>
</td>
</tr>
</tbody>
</table>
<br>
<hr>
<a name="label"></a><h3>Step 2. Select the Label to Use for Automatic Segmentation</h3>
<p>We will be segmenting the caudate nucleus. We have to make sure that
the appropriate combination of the current drawing label and background
(draw over) label is selected.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Make sure that the label <strong>"caudates"</strong> is
selected as the current drawing label</p>
<p>Make sure that <strong>"All Labels"</strong> is selected in
the <strong>Draw over</strong> drop-down box. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="207" width="144"
src="Artwork/ttManualSegmentLabelSubPanel02.gif"></p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>The <strong>draw over</strong> label functions the same way
in automatic segmentation as in manual segmentation. It lets you apply
the results of automatic segmentation to all labels, to all visible
labels, to the clear label, or to a particular label. This gives you a
lot of creative control when segmenting multiple structures. For
instance, to segment a structure that is embedded inside another
structure, you can first segment the outer structure with label <strong>A</strong>
and then segment the inner structure with label <strong>B</strong> and
with the draw-over label set to <strong>A</strong>.</p>
</td>
</tr>
</tbody>
</table>
<br>
<hr>
<h3><a name="select"></a>Step 3. Select the Region of Interest using the Snake Interaction
Mode.</h3>
<p>The automatic segmentation component of SNAP requires a lot of
computer resources. Both the amount of memory and the time required to
compete a segmentation can be reduces by selecting a sub-region of the
image on which to perform segmentation. In this step, we will select a
subregion of the image that contains the caudate nucleus. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Make sure that the slice is fully visible in each the slice
windows by pressing the <strong>Reset View</strong> buttons underneath
the slice windows. </p>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select the snake tool in the IRIS toolbox (shown below) </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="118" width="144"
src="Artwork/ttRegionToolbar.gif"></p>
<p align="left">As you select the snake tool, a pink-colored dashed <em>selection
box </em>will appear at the border of the each slice in the slice
windows, as shown below:</p>
<table cellpadding="5" align="center" border="0" width="10%">
<tbody>
<tr>
<td><img height="212" width="218"
src="Artwork/ttRegionROISelection01.gif"></td>
<td><img height="174" width="224"
src="Artwork/ttRegionROISelection02.gif"></td>
</tr>
</tbody>
</table>
<p>The selection box displays the region of interest that will be used
in automatic segmentation. The use of word <em>region</em> here should
not be confused with <em>region competition</em>. The region of
interest is a rectalinear box, while the regions in region competition
are of arbitrary shape and are defined by uniform intensity. We will
now adjust the region of interest by dragging the sides of the
selection box </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>In one of the slices position the mouse cursor near one of the
corners of the selection box </p>
<p><strong>Hold down</strong> the left mouse button and <strong>drag
</strong>the mouse towards the center of the image. The size of
the box will be adjusted as you move the mouse. </p>
</td>
</tr>
</tbody>
</table>
<p align="left">As you are dragging the selection box, its edges change
color from red to yellow.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Using all three slice windows, adjust the selection box to
include the left and right caudate nuclei. Try to simulate the
selection box in the picture below. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="447" width="532"
src="Artwork/ttRegionROISelectionFinal.gif"></p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>If the selection box disappears in one of the slice windows,
that means that the crosshairs position is outside of the selection
box. You can adjust the crosshairs position in one of the adjacent
slices. </p>
<p>The crosshair position can be adjusted in this mode using the
left mouse button as usual. However, you will need to click a few
pixels away from the selection box to move the crosshairs. </p>
</td>
</tr>
</tbody>
</table>
<p>Notice that the tool options control subpanel contains two buttons: <strong>Reset
Region</strong> and <strong>Segment 3D</strong>. The former is used to
reset the region of interest to the entire image. The second is used to
enter the automatic segmentaiton mode of SNAP. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Once you have adjusted the region of interest, press the <strong>Segment
3D </strong>button.</p>
</td>
</tr>
</tbody>
</table>
<br>
<hr>
<h3 align="left">Step 4. Familiarize Yourself with the Automatic
Segmentation Mode.</h3>
<p align="left">When you press the <strong>Segment 3D </strong>button,
the SnAP user interface changes considerably.</p>
<p align="center"><img height="447" width="532"
src="Artwork/ttRegionNewInterface.gif"></p>
<p align="left">Let's look at some of the new elements that have
appeared:</p>
<ol>
<li>The slice windows have fewer buttons and only show the region of
interest selected in the previous step.<br>
</li>
<li>The IRIS toolbar has been replaced by a smaller toolbar
containing only two buttons. These buttons are used to change the
crosshairs position and to zoom and pan around the region of interest.
The buttons are used in the same way as in the manual SNAP mode that
you are used to, except that fewer options for setting zoom are
provided. <br>
</li>
<li>A large panel labeled "Segmentation Pipeline" appears underneath
the new toolbar. This panel contains the 'wizard ' used for controlling
automatic segmentation. We will work with this wizard extensively in
this section.<br>
</li>
<li>A button labeled <strong>Cancel Segmentation</strong> appears at
the bottom of the control panel. You can use this button at any time to
return to abort the automatic segmentation and return to the manual
SNAP mode. <br>
</li>
<li>A pair of buttons appear underneath the 3D window. These buttons
have the same functionality as the similar looking buttons in the 3D
toolbox in the manual mode.</li>
</ol>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAttention.gif"></td>
<td>
<p>If the image slices appear washed out, i.e., have low
contrast, use the <strong>Intensity Curve</strong> window to change
the contrast as described in <a
href="TutorialSectionViewingImages.html#Curve">Section 3</a>. </p>
</td>
</tr>
</tbody>
</table>
<br>
<hr>
<h3>Step 4. Construct a Region Competition Feature Image.</h3>
<p>Recall the concept of edge and region competition feature images
from the last <a href="TutorialSectionIntroductionToAutomatic.html">section</a>.In
this step we will construct a region competition feature image
appropriate for segmenting the caudate nuclei.</p>
<p>First let's tell SnAP which type of the feature image we will be
using:</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select the option <strong>Intensity Regions</strong> in the
section A of the Segmentation Pipeline Wizard. </p>
</td>
</tr>
</tbody>
</table>
<p>Now, let's estimate the range of intensities to which the voxels in
the caudate nucleus belong.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Move the crosshairs around the caudate nuclei. Look at the
values of the grey level intensity, which is reported in a box labeled <strong>"Grey"</strong>
underneath the toolbar. </p>
</td>
</tr>
</tbody>
</table>
<p>You will find that the intensities in the caudate range between the
high 40's and low 60's. This information is improtant for contructing
the feature image. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Press the button labeled <strong>Preprocess Image...</strong>
This button is used to construct the feature image. The following
window will appear </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="229" width="243"
src="Artwork/ttRegionPreprocessor01.gif"></p>
<p>This window is used to specify the mapping between the greyscale
image intensities and the values of the feature image, which fall into
the range between -1 and 1. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>In the <strong>Intensity Region Filter</strong> window </p>
<ol>
<li>Set the threshold direction to <strong>Below and Above</strong>.</li>
<li>Set the lower threshold to <strong>48</strong>.</li>
<li>Set the upper threshold to <strong>63</strong></li>
<li>Set the smoothness to <strong>1.7</strong></li>
</ol>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>After you use the mouse to click on and move the knobs that
are used to change the threshold and smoothness values, you can use the<strong>
left and right arrow keys</strong> to move these knobs one value at a
time. </p>
</td>
</tr>
</tbody>
</table>
<p>As soon as you change some of the parameters, the SnAP slice windows
will display the feature image instead of the grey image. As you change
the parameters, the slice windows are updated immideately. If you
uncheck the <strong>Preview result</strong> checkbox, the slice
windows will only reflect the values of the parameters when you press
the <strong>Apply</strong> button. </p>
<p>Our goal in setting the parameters is to make sure that the voxels
inside of fthe caudate nuclei are assigned positive values in the
feature image, and that the voxels outside of it are assigned negative
values. There are two ways to check that this happens:</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>Move the crosshairs around in the slice windows (the
intensity region filter window will remain on top). Look at the values
of the feature image, which are reported in a box labeled <strong>"Preproc"</strong>
underneath the toolbar. </td>
</tr>
</tbody>
</table>
<p>or</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Check the <strong>Combined Display</strong> check box. The
greylevel image is shown again, but the pixels where the feature image
is positive are painted over with the color of the current segmentation
label, as shown below. This is an easy way to make sure that the pixels
in the caudate have a positive feature image value. </p>
<p>Uncheck <strong>Combined Display</strong> check box to see
the feature image again. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="223" width="266"
src="Artwork/ttRegionPreprocessor02.gif"></p>
<p>The smoothness value determines the steepness of the mapping curve.
It does not affect the sign of the feature function at any particular
voxel, but it does have an effect on the smoothness of the snake
evolution. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>When you are satisfied with the feature image, press <strong>Okay</strong>
to compute the feature image at all voxels and close the intensity
region filter window. </td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>SnAP lets you save and load feature images. Just use the
appropriate menu items in the <strong>File</strong> menu. You can also
load feature images by pressing the <strong>Load from File... </strong>button
in the segmentation pipeline wizard.</p>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconExpert.gif"></td>
<td>
<p>Voxels in feature images are saved as floating point numbers,
so some applications may not be able to load the saved images. You can
not save feature images in GIPL format because if does not support
floating point voxels. The Meta format is recommended. </p>
</td>
</tr>
</tbody>
</table>
<p>We are now almost done with the first step of the Segmentation
Pipeline Wizard.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>Press the <strong>Next </strong>button in the Segmentation
Pipeline Wizard to proceed to the next step.</td>
</tr>
</tbody>
</table>
<br>
<hr>
<h3><a name="bubbles"></a>Step 5. Initialize the Snake with Bubbles</h3>
<p>The Segmentation Pipeline Wizard should be displaying "Step 2 od 3",
as shown below.</p>
<p align="center"><img height="382" width="144"
src="Artwork/ttRegionWizard02.gif"></p>
<p>This step of the wizard is used to position spherical bubbles to
that initialize the snake, as described in the previous <a
href="TutorialSectionIntroductionToAutomatic.html#Init">section</a>. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Move the crosshairs such that the crosshairs position is
inside of the right caudate nucleus in all three slice windows.</p>
<p>Press the <strong>Add Bubble </strong>button to place a
bubble at the crosshairs position. </p>
<p>Use the <strong>Radius </strong>slider to change the radius
of the bubble.</p>
</td>
</tr>
</tbody>
</table>
<p>After adding a bubble, the SnAP window should look like this:</p>
<p align="center"><img height="223" width="266"
src="Artwork/ttRegionAddBubble01.gif"></p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Place one more bubble inside the right caudate and place two
bubbles inside the left caudate. </p>
</td>
</tr>
</tbody>
</table>
<p>The result should look something like this: </p>
<p align="center"><img height="223" width="266"
src="Artwork/ttRegionAddBubble02.gif"></p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>To remove a bubble, select it in the list of bubbles
underneath the <strong>Radius</strong> slider and press the <strong>Remove
bubble</strong> button. </p>
</td>
</tr>
</tbody>
</table>
<p>Finally, </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>Press the <strong>Next </strong>button in the Segmentation
Pipeline Wizard to proceed to the next step.</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>As an alternative to using bubbles, you can use manual
segmentation to initialize the snake. Before starting automatic
segmentation, create a manual segmentation as described in <a
href="TutorialSectionManualSegmentation.html">Section 4</a> using the
same label that you wish to use for snake segmentation. The manual
segmentation will be used as the snake initialization, and you would
not have to add any bubbles. </p>
</td>
</tr>
</tbody>
</table>
<br>
<hr>
<h3>Step 6. Run the Snake Evolution </h3>
<p>The Segmentation Pipeline Wizard should be displaying "Step 3 od 3",
as shown below. </p>
<p align="center"><img height="382" width="144"
src="Artwork/ttRegionWizard03.gif"></p>
<p>This wizard page allows you to set the parameters for snake
evolution, and it allows you to control the snake using VCR-style
controls. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Press <strong>Set Parameters...</strong> to open the snake
parameter window.</p>
</td>
</tr>
</tbody>
</table>
<p>The Snake Parameters window is shown below. This window consists of
two parts. On the left is a control panel used to specify various
parameters, mainly the weights of the propagation, curvature, and
advection forces that were discussed in <a
href="TutorialSectionIntroductionToAutomatic.html#Velocity">Section 5</a>.
These velocities are displayed using a fixed feature image, and not the
feature image that you are working with. Nevertheless, this image is
useful for understanding the relative contribution of the forces to
snake evolution</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>
The red curve for which the velocities are shown can be changed using the mouse. Left-click once in one of the four windows showing the curve and yellow 'control points' will appear. Move the control points by dragging using with the left mouse button. Try moving the curve and see how the foces change.</p>
</td>
</tr>
</tbody>
</table>
<p>The snake parameter window also lets you save snake evolution
parameter settings to a file and to load them from a file.</p>
<p align="center"><img height="287" width="433"
src="Artwork/ttRegionParameterWindow.gif"></p>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Change the curvature velocity weight to from <strong>0.20 </strong>
to <strong>0.15</strong> </p>
<p>Press <strong>Accept</strong> to close the window</p>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconExpert.gif"></td>
<td>
<p>The <strong>Mathematical Mode</strong> tab of the Snake
Parameters Window shows mathematical expression for the partial
differential equation that drives the snake evolution, and allows you
to set the parameters directly as constants in this equation.</p>
<p>You can also choose to display the <strong>experimental
equation</strong>, which contains more terms and gives you more control
over snake evolution. </p>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconExpert.gif"></td>
<td>
<p>The <strong>Advanced Mode</strong> tab of the Snake
Parameters Window is discussed in the section on <a
href="TutorialSectionTipsAndTricks.html#AdvancedParms">Tips and Tricks</a>.
It can be used to speed up large segmentations.</p>
</td>
</tr>
</tbody>
</table>
<p align="left">Now that we've set the snake parameters, we are ready
to run the snake evolution. Notice the VCR-style controls located in
the Segmentation Pipeline Wizard. </p>
<p align="center"><img height="382" width="144"
src="Artwork/ttRegionWizard03.gif"></p>
<p align="left">These controls have the following functionality:</p>
<ul>
<li>The leftmost control is used to <strong>rewind </strong>the
snake after it had been evolving for some time.</li>
<li>The second control is used to <strong>run</strong> the snake
until stopped.</li>
<li>The third control is used to <strong>stop</strong> the running
snake</li>
<li>The rightmost control is used to <strong>step</strong> the
snake, i.e., to run for a fixed number of iterations.</li>
</ul>
<p>Underneath the VCR buttons is a control that allows you to set the
size of the step used in snake evolution. The larger the step value,
the fewer times will the user interface be updated as the snake
evolves. For small segmentations, it is advisable to leave the step
size at 1. Next to the step size dropbox is a display that shows the
current iteration. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Press the <strong>Step </strong> button several times to run
the snake for a few iterations</p>
<p>Press the <strong>Run </strong>button once and watch the
snake fill up the caudates.</p>
<p>Press the <strong>Stop </strong> button when the caudates
have been filled up </p>
<p>Press the <strong>Rewind</strong> button if you want to
restart.</p>
</td>
</tr>
</tbody>
</table>
<p>To see the segmentation result in 3D, you can press the <strong>Update
Mesh </strong> button underneath the 3D window, or you can select the <strong>Update
Continuously </strong>checkbox.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAttention.gif"></td>
<td>
<p>Warning! Selecting <strong>Update Continuously</strong> will
degrade segmentation performace significantly, possibly by orders of
magnitude!</p>
</td>
</tr>
</tbody>
</table>
<p>The result of the segmentation should look something like this. </p>
<p align="center"><img height="223" width="266"
src="Artwork/ttRegionResult.gif"></p>
<hr>
<h3>Step 7. Finalize the Segmentation </h3>
<p>The final step in the automatic segmentation process is to return to
the SNAP manual segmentation mode, incorporating the segmentation
results with other structures that have been previously segmented.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Press the <strong>Finish</strong> button in the Segmentation
Pipeline Wizard</p>
</td>
</tr>
</tbody>
</table>
<p>The Segmentation Pipeline Wizard will disappear, and the layout of
the SNAP control panel will return to normal. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p><strong>[Optional]</strong> Save your segmentation as
described in <a href="TutorialSectionManualSegmentation.html#Save">Section
4</a>. </p>
</td>
</tr>
</tbody>
</table>
<br>
<hr>
<h3>Step 8. Use the 3D Tools to Edit the Segmentation Results </h3>
<p>In this step we will postprocess the results of the segmentation
using 3D tools. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Press the <strong>Update Mesh </strong> button below the 3D
window to render the results </p>
</td>
</tr>
</tbody>
</table>
<br>
<p align="left">Now, let us examine the different tools available in
the <strong>3D Toolbox</strong>, which is shown below.</p>
<p align="center"><img height="121" width="142"
src="Artwork/ttRegion3DTools.gif"></p>
<p align="left">The toolbox contains four tools. Top to bottom, left to
right, they are </p>
<ul>
<li><strong>3D Trackball Tool</strong>: Used to rotate, zoom, and pan
in the 3D window.</li>
<li><strong>3D Crosshair Tool:</strong> Used to set the crosshair
location by clicking on anatomical structures shown in the 3D window</li>
<li><strong>3D Scalpel Tool:</strong> Used to repaint or erase parts
of the anatomical structures shown in the 3D window</li>
<li><strong>3D Spray Paint Tool</strong>: Used to add anatomical
landmarks to the surface of anatomical structures shown in the 3D window</li>
</ul>
<p>Let's begin by examining the 3D trackball tool:</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select the <strong>3D Trackball Tool</strong></p>
<p>Press and hold the <strong>left mouse button </strong>and
move the mouse to rotate the 3D view.</p>
<p>Press and hold the <strong>right mouse button </strong>and
move the mouse up or down to zoom in and out in the 3D view</p>
<p>Press and hold the <strong>middle mouse button</strong> and
move the mouse to pan in the 3D view. </p>
</td>
</tr>
</tbody>
</table>
<p>Now try the 3D crosshair tool: </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select the <strong>3D Crosshair Tool</strong></p>
<p>Position the mouse over any point on the caudates and click
the <strong>left mouse button</strong>. The crosshair position will
move to the selected point and the slices shown in the slice windows
will be changed.</p>
</td>
</tr>
</tbody>
</table>
<p>Now, something more complex. We will use the 3D scalpel tool to
assign different labels to the left and right caudate nuclei. </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Use the <strong>Edit Labels </strong>button to add two new
labels called 'left caudate' and 'right caudate' with different colors
(for information on editing labels, see <a
href="TutorialSectionManualSegmentation.html#EditLabel">Section 3</a>).
</p>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select 'right caudate' as the current drawing label, and
select 'caudates' (the label used for automatic segmentation) as the
label to draw over, as shown below. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="209" width="142"
src="Artwork/ttRegionScalpelLabels.gif"></p>
<p>The 3D scalpel tool works by partitioning the space into two regions
separated by a plane. The segmentation labels on one side of the plane
are replaced by the current drawing label, as long as they agree with
the current setting of the draw over label. In order to use the scalpel
tool, we need to first rotate the 3D view such that a line can be drawn
between the two caudates.</p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Use the <strong>3D Trackball</strong> tool to rotate the 3D
view in such a way that the caudates can be separated by an imaginary
line, as shown below. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="212" width="217"
src="Artwork/ttRegion3DImaginaryLine.gif"></p>
<p align="left">Now, we will use the 3D scalpel tool to actually draw a
line in place of the imaginary line </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Select the <strong>3D Scalpel Tool</strong></p>
<p>Click the <strong>left mouse button</strong> at one end of
the imaginary line separating the caudates</p>
<p>Move the mouse around the 3D window. You will see a white line
indicating where the 'cut' will be made, and an arrow indicating which
half of the space will be relabeled.</p>
<p>Click the <strong>left mouse button</strong> again at the
other end of the imaginary line </p>
</td>
</tr>
</tbody>
</table>
<p align="left">The result of this operation should look like this:</p>
<p align="center"><img height="213" width="218"
src="Artwork/ttRegion3DScalpelLine.gif"> </p>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconTip.gif"></td>
<td>
<p>If you are not satisfied with the 'cut', press the <strong>Reset
View</strong> button and try again.</p>
</td>
</tr>
</tbody>
</table>
<br>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Otherwise, press the <strong>Accept</strong> button to
repaint one of the caudates with the active drawing label and press the
<strong>Update Mesh</strong> to see the result in 3D. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="213" width="218"
src="Artwork/ttRegion3DScalpelResult.gif"></p>
<p align="left">The 3D scalpel is a very powerful tool for editing
segmentation results. Using the clear label as the active drawing
label, you can erase parts of the segmentation that have leaked outside
of the caudates. </p>
<hr>
<h3>Step 9. [Optional] Segment the Ventricles</h3>
<table cellspacing="0" cellpadding="4" align="center" border="1"
width="80%">
<tbody>
<tr>
<td valign="top" width="36"><img height="36" width="36"
src="Artwork/ttIconAction.gif"></td>
<td>
<p>Use the procedure outlined in the steps above to segment the
ventricles in the image. You will need to use the <strong>Above</strong>
threshold direction setting when creating the feature image. </p>
</td>
</tr>
</tbody>
</table>
<p align="center"><img height="229" width="243"
src="Artwork/ttRegionFunctionForVentricles.gif"></p>
<p align="left">The result should look like this</p>
<p align="center"><img height="213" width="218"
src="Artwork/ttRegionVentricleResult.gif"> </p>
</body>
</html>
|
