Hi everybody, I have a problem with running the program .

Hi everybody, I have a problem with running the program .

there is an error like this ???

Index exceeds matrix dimensions.

in this four instructions

imagesTrain = reshape (images(:,:,:,indsTrain),insz(1),insz(2),[]);
imagesVal   = reshape(images(:,:,:,indsVal),  insz(1),insz(2),[]);   
labelsTrain = reshape(labels(:,:,:,indsTrain),insz(1),insz(2),[]);
labelsVal   = reshape(labels(:,:,:,indsVal),  insz(1),insz(2),[]);

How is the solution of the error?

[Walter Roberson]

what is size(images), size(labels), size(insz) ? What are the values of indsTrain and indsVal ?

[Image Analyst]

Why are you trying to reshape these arrays? Do you just want to extract them instead?

[Jan]

Please post a complete copy of the error message. The partial message is not enough to indentify the problem. Perhaps you have redefined reshape = 17 or indsTrain is greater than size(images, 4) ??

[Stephen23]

mosbahi sourour's "Answer" moved here and formatted correctly:

This is the program :

functionimdb=setupImdbIBSRv2(net,indsTrain,indsVal,augment,view)

if nargin < 2, indsTrain = 1:5; end  if nargin < 3, indsVal   = [];  end  
if nargin < 4, augment   = true;end  
if nargin < 5, view      = 1;   end  
% Read original patches
switch view
    case {1,'axial'}
        permvec = [1 2 3];
    case {2, 'sagittal'} 
        permvec = [2 3 1];
    case {3, 'coronal'} 
        permvec = [3 1 2];
    otherwise
        error('Invalid view')
end
paths    = setPaths();
dirs     = dir(paths.IBSR); dirs = dirs(~ismember({dirs.name},{'.','..','.DS_Store','README.txt'}));
nFiles   = numel(dirs);  assert(nFiles == 18);
insz     = [256,128,256]; 
insz     = insz(permvec); nChannelsPerVolume = insz(3); 
images   = zeros(insz(1),insz(2),nChannelsPerVolume,nFiles, 'uint8');
labels   = zeros(insz(1),insz(2),nChannelsPerVolume,nFiles, 'uint8');
tmpSeg   = zeros(insz(1),insz(2),nChannelsPerVolume, 'uint8');
ibsrLabels = [0,2,3,4,5,7,8,10,11,12,13,14,15,16,17,18,24,26,28,29,30,41,...
    42,43,44,46,47,48,49,50,51,52,53,54,58,60,61,62,72];
labelMap = containers.Map(ibsrLabels,0:numel(ibsrLabels)-1);
ticStart = tic;
for i=1:nFiles
    imgPath = fullfile(paths.IBSR, dirs(i).name, [dirs(i).name '_ana_strip.nii']);
    segPath = fullfile(paths.IBSR, dirs(i).name, [dirs(i).name '_seg_ana.nii']);
    if ~exist(imgPath,'file') && exist([imgPath '.gz'],'file')
        gunzip([imgPath '.gz']);
    end
    if ~exist(segPath,'file') && exist([segPath '.gz'],'file')
        gunzip([segPath '.gz']);
    end
    img = load_nii(imgPath);
    seg = load_nii(segPath);
    img.img = permute(img.img, permvec);
    seg.img = permute(seg.img, permvec);
    assert(size(img.img,3) == nChannelsPerVolume)
    tmpSeg(:) = 0;
    for j=1:numel(ibsrLabels)
        tmpSeg(seg.img == ibsrLabels(j)) = labelMap(ibsrLabels(j));
    end
    images(:,:,:,i) = 255*bsxfun(@rdivide,single(img.img), single(max(max(img.img))));
    labels(:,:,:,i) = tmpSeg;
    progress('Reading ISBR images',i,nFiles,ticStart);
end

imagesTrain = reshape (images(:,:,:,indsTrain),insz(1),insz(2),[]);
imagesVal   = reshape(images(:,:,:,indsVal),  insz(1),insz(2),[]); clear images;
labelsTrain = reshape(labels(:,:,:,indsTrain),insz(1),insz(2),[]);
labelsVal   = reshape(labels(:,:,:,indsVal),  insz(1),insz(2),[]); clear labels;
assert(size(imagesTrain,3) == numel(indsTrain) * nChannelsPerVolume);
assert(size(imagesVal  ,3) == numel(indsVal) * nChannelsPerVolume)
complete copy of the error message
Index exceeds matrix dimensions.

Error in cnn>setupImdbIBSRv2 (line 179)
imagesTrain = reshape (images(:,:,:,indsTrain),insz(1),insz(2),[]);

[Jan]

And the complete error message is? We need to know at least the failing line.

Answer 1

[John D'Errico]

When you get the error, what is the shape of images, and insz?

size(images)
size(insz)

Also, what are the values of indsTrain and indsval at that time?

One of those variables is not the size you are expecting it to be.

I cannot answer your question, because I cannot run your code as you ran it. I don't have the input arguments, nor do I know what you passed into the function. But you can determine all of this easily.

The trick is to use the debugger. Set this flag at the command line, then run your code. That will have the debugger stop when it sees an error, and then you can do the tests I showed above. That will give you everything you need to answer the question yourself.

dbstop if error

[mosbahi sourour]

the programme in this link https://github.com/tsogkas/brainseg

the name of program CNN. m

[John D'Errico]

I told you what to do, how to debug the problem. Only you can do the rest.