Invalid training data. The output size ([128 128 140 2]) of the last layer does not match the response size ([128 128 36 2]).

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Dear All,
I have develop code for 3D U-Net. But got error when want train.
This is my code 3D U-Net. The Data can get thru this link https://drive.google.com/drive/folders/1cbKwpP8P8oblAs4_geDpRUcg8Y3IEu_j?usp=share_link
clc
clear all
close all
%testDataimages
DATASetDir = fullfile('C:\Users\USER\Downloads\HEAD & NECK\HEAD & NECK');
IMAGEDir = fullfile(DATASetDir,'ImagesTr');
volReader = @(x) matRead(x);
volds = imageDatastore(IMAGEDir, ...
'FileExtensions','.mat','ReadFcn',volReader);
% labelReader = @(x) matread(x);
matFileDir = fullfile('C:\Users\USER\Downloads\HEAD & NECK\HEAD & NECK\LabelsTr');
classNames = ["background", "tumor"];
pixelLabelID = [0 1];
% pxds = (LabelDirr,classNames,pixelLabelID, ...
% 'FileExtensions','.mat','ReadFcn',labelReader);
pxds = pixelLabelDatastore(matFileDir,classNames,pixelLabelID, ...
'FileExtensions','.mat','ReadFcn',@matRead);
volume = preview(volds);
label = preview(pxds);
volumeViewer(volume, label)
patchSize = [128 128 36];
patchPerImage = 16;
miniBatchSize = 8;
patchds = randomPatchExtractionDatastore(volds,pxds,patchSize, ...
'PatchesPerImage',patchPerImage);
patchds.MiniBatchSize = miniBatchSize;
dsTrain = transform(patchds,@augment3dPatch);
volLocVal = fullfile('C:\Users\USER\Downloads\HEAD & NECK\HEAD & NECK\ImagesVal');
voldsVal = imageDatastore(volLocVal, ...
'FileExtensions','.mat','ReadFcn',volReader);
lblLocVal = fullfile('C:\Users\USER\Downloads\HEAD & NECK\HEAD & NECK\LabelsVal');
pxdsVal = pixelLabelDatastore(lblLocVal,classNames,pixelLabelID, ...
'FileExtensions','.mat','ReadFcn',volReader);
dsVal = randomPatchExtractionDatastore(voldsVal,pxdsVal,patchSize, ...
'PatchesPerImage',patchPerImage);
dsVal.MiniBatchSize = miniBatchSize;
lgraph = layerGraph();
tempLayers = [
image3dInputLayer([128 128 36 1],"Name","image3dinput")
convolution3dLayer([3 3 3],64,"Name","Encoder-Stage-1-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Encoder-Stage-1-ReLU-1")
convolution3dLayer([3 3 3],64,"Name","Encoder-Stage-1-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Encoder-Stage-1-ReLU-2")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
maxPooling3dLayer([2 2 2],"Name","Encoder-Stage-1-MaxPool","Stride",[2 2 2])
convolution3dLayer([3 3 3],128,"Name","Encoder-Stage-2-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Encoder-Stage-2-ReLU-1")
convolution3dLayer([3 3 3],128,"Name","Encoder-Stage-2-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Encoder-Stage-2-ReLU-2")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
maxPooling3dLayer([2 2 2],"Name","Encoder-Stage-2-MaxPool","Stride",[2 2 2])
convolution3dLayer([3 3 3],256,"Name","Encoder-Stage-3-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Encoder-Stage-3-ReLU-1")
convolution3dLayer([3 3 3],256,"Name","Encoder-Stage-3-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Encoder-Stage-3-ReLU-2")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
dropoutLayer(0.5,"Name","Encoder-Stage-3-DropOut")
maxPooling3dLayer([2 2 2],"Name","Encoder-Stage-3-MaxPool","Stride",[2 2 2])
convolution3dLayer([3 3 3],512,"Name","Bridge-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Bridge-ReLU-1")
convolution3dLayer([3 3 3],512,"Name","Bridge-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Bridge-ReLU-2")
dropoutLayer(0.5,"Name","Bridge-DropOut")
transposedConv3dLayer([2 2 2],256,"Name","Decoder-Stage-1-UpConv","BiasLearnRateFactor",2,"Stride",[2 2 2],"WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-1-UpReLU")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
depthConcatenationLayer(2,"Name","Decoder-Stage-1-DepthConcatenation")
convolution3dLayer([3 3 3],256,"Name","Decoder-Stage-1-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-1-ReLU-1")
convolution3dLayer([3 3 3],256,"Name","Decoder-Stage-1-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-1-ReLU-2")
transposedConv3dLayer([2 2 2],128,"Name","Decoder-Stage-2-UpConv","BiasLearnRateFactor",2,"Stride",[2 2 2])
reluLayer("Name","Decoder-Stage-2-UpReLU")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
depthConcatenationLayer(2,"Name","Decoder-Stage-2-DepthConcatenation")
convolution3dLayer([3 3 3],128,"Name","Decoder-Stage-2-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-2-ReLU-1")
convolution3dLayer([3 3 3],128,"Name","Decoder-Stage-2-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-2-ReLU-2")
transposedConv3dLayer([2 2 2],64,"Name","Decoder-Stage-3-UpConv","BiasLearnRateFactor",2,"Stride",[2 2 2],"WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-3-UpReLU")];
lgraph = addLayers(lgraph,tempLayers);
tempLayers = [
depthConcatenationLayer(2,"Name","Decoder-Stage-3-DepthConcatenation")
convolution3dLayer([3 3 3],64,"Name","Decoder-Stage-3-Conv-1","Padding","same","WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-3-ReLU-1")
convolution3dLayer([3 3 3],64,"Name","Decoder-Stage-3-Conv-2","Padding","same","WeightsInitializer","he")
reluLayer("Name","Decoder-Stage-3-ReLU-2")
convolution3dLayer([1 1 1],2,"Name","Final-ConvolutionLayer","Padding","same","WeightsInitializer","he")
softmaxLayer("Name","Softmax-Layer")
pixelClassificationLayer("Name","Segmentation-Layer")];
lgraph = addLayers(lgraph,tempLayers);
% clean up helper variable
clear tempLayers;
lgraph = connectLayers(lgraph,"Encoder-Stage-1-ReLU-2","Encoder-Stage-1-MaxPool");
lgraph = connectLayers(lgraph,"Encoder-Stage-1-ReLU-2","Decoder-Stage-3-DepthConcatenation/in2");
lgraph = connectLayers(lgraph,"Encoder-Stage-2-ReLU-2","Encoder-Stage-2-MaxPool");
lgraph = connectLayers(lgraph,"Encoder-Stage-2-ReLU-2","Decoder-Stage-2-DepthConcatenation/in2");
lgraph = connectLayers(lgraph,"Encoder-Stage-3-ReLU-2","Encoder-Stage-3-DropOut");
lgraph = connectLayers(lgraph,"Encoder-Stage-3-ReLU-2","Decoder-Stage-1-DepthConcatenation/in2");
lgraph = connectLayers(lgraph,"Decoder-Stage-1-UpReLU","Decoder-Stage-1-DepthConcatenation/in1");
lgraph = connectLayers(lgraph,"Decoder-Stage-2-UpReLU","Decoder-Stage-2-DepthConcatenation/in1");
lgraph = connectLayers(lgraph,"Decoder-Stage-3-UpReLU","Decoder-Stage-3-DepthConcatenation/in1");
plot(lgraph);
options = trainingOptions('sgdm', ...
'MiniBatchSize',1, ...
'MaxEpochs',100, ...
'InitialLearnRate',1e-3, ...
'Shuffle','every-epoch', ...
'ValidationData',dsVal, ...
'ValidationFrequency',200, ...
'Verbose',false, ...
'Plots','training-progress', ...
'ExecutionEnvironment','cpu');
doTraining = true;
if doTraining
modelDateTime = datestr(now,'dd-mmm-yyyy-HH-MM-SS');
[net,info] = trainNetwork(dsTrain,lgraph,options);
save(['trained3DUNet-' modelDateTime '-Epoch-' num2str(maxEpochs) '.mat'],'net');
else
load('trained3DVNet-07-Jun-2022-13-45-30-Epoch-250.mat');
end
This is my ERROR
Error using trainNetwork
Invalid training data. The output size ([128 128 140 2]) of the last layer does not match the response size ([128 128 36
2]).
  4 comentarios
Amanjit Dulai
Amanjit Dulai el 8 de Nov. de 2022
The labels are being loaded with size [128 128 140 2]. This is being done by the function matRead which is specified as an input when creating the variable pxds. But this function is not included in your code above. Do you have the code for this function?

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