Index exceeds the number of array elements. Index must not exceed 0.

clc;
clear all;
fpath='/MATLAB Drive/HGG';
filepath=fullfile(fpath,'A');
imageDir = fullfile(fpath,'A');
labelDir = fullfile(fpath,'A');
imds = imageDatastore(imageDir,'IncludeSubfolders',true,'FileExtensions','.nii','ReadFcn',@(x) niftiread(x));
classNames = ["background","tumor"];
pixelLabelID = [0 1];
pxds = pixelLabelDatastore(labelDir,classNames,pixelLabelID,'FileExtensions','.nii','ReadFcn',@(x) niftiread(x));
patchSize = [132 132 132];
patchPerImage = 16;
miniBatchSize = 8;
patchds = randomPatchExtractionDatastore(imds,pxds,patchSize,'PatchesPerImage',patchPerImage);
patchds.MiniBatchSize = miniBatchSize;

dsTrain = transform(patchVolDS,@(x) preprocessVolumetricPatchDS(x));
minibatch = read(dsTrain)

function data = niftiread(x)
    data = niftiread(x);
if ndims(data) == 3
    data = rgb2gray(data);
end
data = im2uint8(mat2gray(data));
end

function batchOut = preprocessVolumetricPatchDS(batchIn)

numRows = size(batchIn,1); 
batchOut = batchIn;

% 5 augmentations: nil,rot90,fliplr,flipud,rot90(fliplr)
augType = {@(x) x,@rot90,@fliplr,@flipud,@(x) rot90(fliplr(x))};

for idx = 1:numRows

    img = batchIn{idx,1}{1};
    resp = batchIn{idx,2}{1};
    
    rndIdx = randi(5,1);
    imgAug = augType{rndIdx}(img);
    respAug = augType{rndIdx}(resp);
    
    batchOut(idx,:) = {imgAug,respAug};

end
end


Error 

Error using matlab.io.datastore.ImageDatastore/readimage (line 32)
Index exceeds the number of array elements. Index must not exceed 0.

Error in matlab.io.datastore.PixelLabelDatastore/readimage (line 574)
                [C, info] = readimage(this.ImageDatastore,i);

Error in matlab.io.datastore.PixelLabelDatastore/preview (line 407)
            C = readimage(this,1);

Error in randomPatchExtractionDatastore (line 325)
                this.NumPixelLabelsDims = ndims(preview(this.dsSecondInternal));

Error in Suntitled (line 14)
patchds = randomPatchExtractionDatastore(imds,pxds,patchSize,'PatchesPerImage',patchPerImage);
 

[Walter Roberson]

What happens if imds is empty? If no images are found?

[Max Walliam]

there are images .nii format and the error is

Index exceeds the number of array elements. Index must not exceed 0

[Walter Roberson]

There are no .nii files being found in /MATLAB Drive/HGG/A or any subdirectory of that directory.

Answer 1

[yanqi liu]

sir，may be check the data folder，such as

clc;
clear all;
fpath='/MATLAB Drive/HGG';

filepath=fullfile(fpath,'A');
imageDir = fullfile(fpath,'A');
labelDir = fullfile(fpath,'A');

fs = ls(fulfile(imageDir, '*.nii'));
disp(fs)

fs2 = ls(fulfile(labelDir, '*.nii'));
disp(fs2)