Segment3DBrainTumorUsingDeepLearningExample/DeepMedic Segment at master · ImageGuidedTherapyLab/Segment3DBrainTumorUsingDeepLearningExample · GitHub

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
% create network object
lgraph = layerGraph();

% create layers
tempLayers = image3dInputLayer([57 57 57 4],"Name","image3dinput");
lgraph = addLayers(lgraph,tempLayers);

tempLayers = convolution3dLayer([17 17 17],1,"Name","CropSizeAdjuster","BiasLearnRateFactor",0,"Padding",[4 4 4;4 4 4],"Stride",[2 2 2],"WeightL2Factor",0,"WeightLearnRateFactor",0);
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    averagePooling3dLayer([3 3 3],"Name","avgpool3d","Stride",[3 3 3])
    batchNormalizationLayer("Name","batchnorm_4")
    reluLayer("Name","relu_4")
    convolution3dLayer([3 3 3],30,"Name","conv3d_5")
    batchNormalizationLayer("Name","batchnorm_5")
    reluLayer("Name","relu_5")
    convolution3dLayer([3 3 3],30,"Name","conv3d_6")
    batchNormalizationLayer("Name","batchnorm_6")
    reluLayer("Name","relu_6")
    convolution3dLayer([3 3 3],40,"Name","conv3d_4")
    batchNormalizationLayer("Name","batchnorm_8")
    reluLayer("Name","relu_7")
    convolution3dLayer([3 3 3],40,"Name","conv3d_8")
    batchNormalizationLayer("Name","batchnorm_9")
    reluLayer("Name","relu_8")
    convolution3dLayer([3 3 3],40,"Name","conv3d_9")
    batchNormalizationLayer("Name","batchnorm_10")
    reluLayer("Name","relu_9")
    convolution3dLayer([3 3 3],40,"Name","conv3d_10")
    batchNormalizationLayer("Name","batchnorm_11")
    reluLayer("Name","relu_10")
    convolution3dLayer([3 3 3],50,"Name","conv3d_11")
    batchNormalizationLayer("Name","batchnorm_12")
    reluLayer("Name","relu_11")
    convolution3dLayer([3 3 3],50,"Name","conv3d_12")
    transposedConv3dLayer([7 7 7],50,"Name","upsample","BiasLearnRateFactor",0,"WeightL2Factor",0,"WeightLearnRateFactor",0)];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    crop3dLayer("Name","crop3d")
    batchNormalizationLayer("Name","batchnorm_1")
    reluLayer("Name","relu_1")
    convolution3dLayer([3 3 3],30,"Name","conv3d_1")
    batchNormalizationLayer("Name","batchnorm_2")
    reluLayer("Name","relu_2")
    convolution3dLayer([3 3 3],30,"Name","conv3d_2")
    batchNormalizationLayer("Name","batchnorm_3")
    reluLayer("Name","relu_3")
    convolution3dLayer([3 3 3],40,"Name","conv3d_3")
    batchNormalizationLayer("Name","batchnorm_13")
    reluLayer("Name","relu_12")
    convolution3dLayer([3 3 3],40,"Name","conv3d_14")
    batchNormalizationLayer("Name","batchnorm_14")
    reluLayer("Name","relu_13")
    convolution3dLayer([3 3 3],40,"Name","conv3d_15")
    batchNormalizationLayer("Name","batchnorm_15")
    reluLayer("Name","relu_14")
    convolution3dLayer([3 3 3],40,"Name","conv3d_16")
    batchNormalizationLayer("Name","batchnorm_16")
    reluLayer("Name","relu_15")
    convolution3dLayer([3 3 3],50,"Name","conv3d_17")
    batchNormalizationLayer("Name","batchnorm_17")
    reluLayer("Name","relu_16")
    convolution3dLayer([3 3 3],50,"Name","conv3d_13")];
lgraph = addLayers(lgraph,tempLayers);

tempLayers = [
    concatenationLayer(4,2,"Name","concat")
    batchNormalizationLayer("Name","batchnorm_7")
    reluLayer("Name","relu_17")
    convolution3dLayer([1 1 1],150,"Name","conv3d_7")
    batchNormalizationLayer("Name","batchnorm_18")
    reluLayer("Name","relu_19")
    convolution3dLayer([1 1 1],150,"Name","conv3d_18","BiasLearnRateFactor",0)
    batchNormalizationLayer("Name","batchnorm")
    convolution3dLayer([1 1 1],2,"Name","conv3d")
    softmaxLayer("Name","softmax")
    dicePixelClassificationLayer("Name","dice-pixel-class")];
lgraph = addLayers(lgraph,tempLayers);

% clean up helper variable
clear tempLayers;

% connect layers
lgraph = connectLayers(lgraph,"image3dinput","CropSizeAdjuster");
lgraph = connectLayers(lgraph,"image3dinput","avgpool3d");
lgraph = connectLayers(lgraph,"image3dinput","crop3d/in");
lgraph = connectLayers(lgraph,"CropSizeAdjuster","crop3d/ref");
lgraph = connectLayers(lgraph,"conv3d_13","concat/in2");
lgraph = connectLayers(lgraph,"upsample","concat/in1");

plot(lgraph);