I am converting a 3D image to a set of 2D images(slices), but the images I receive are not of good quality, so there is a loss of information. Is there a solution? please help

clear all;

close all;

i=niftiinfo('picture.nii');

Va = niftiread(i);

Vmax = max(Va);

Vmin = min(Va);

Va_prime = ((Va-abs(Vmin))./(Vmax-Vmin))*255;%Normalisation -> valeurs entre 0 et 1

dim = size(Va_prime);%Dimensions du volume

volumeViewer(Va)

[sliceX sliceY sliceZ]=size(Va);

frontal = Va_prime(:,:,sliceZ);

sagittal = reshape(Va_prime(sliceX,:,:),[dim(2) dim(3)]);

horizontal = reshape(Va_prime(:,sliceY,:),[dim(1) dim(3)]);

folder='direction file';

for i=1:sliceY

frontal=uint8(Va(:,:,i));

frontal=imrotate(frontal,90);

basefilename=sprintf('image %d.png',i);

fullfilemane=fullfile(folder,basefilename);

imshow(frontal)

imwrite(frontal, fullfilemane);

end

Answer 1

[DGM]

Well here goes. I'm pretty sure the main problems were in the normalization, but there were other issues that could be simplified anyway. I left the unused stuff in there with notes.

% i have no idea what your image is
ni=niftiinfo('brain.nii');
Va = niftiread(ni);

% if Va is 3D, min(Va) will return a 2D array
% since it only minimizes along dim1.  is that desired?
%Vmax = max(Va); 
%Vmin = min(Va);
% for the global minimum instead (see below why neither are used)
%Vmax = max(Va(:)); 
%Vmin = min(Va(:));

%Va_prime = ((Va-abs(Vmin))./(Vmax-Vmin))*255; % that's not normalization
Va_prime = mat2gray(Va); % this normalizes independent of image class

%dim = size(Va_prime); % this contains the same information as sliceX/Y/Z
%[sliceX sliceY sliceZ]=size(Va); % so just use them instead
% again, don't really need to use either though

% you're picking only one slice each (the last one)... why?
%frontal = Va_prime(:,:,sliceZ); 
%sagittal = reshape(Va_prime(sliceX,:,:),[sliceY sliceZ]);
%horizontal = reshape(Va_prime(:,sliceY,:),[sliceX sliceZ]); 

% i don't know the orientation of your image, so i'm guessing which side is which
% but using permute() avoids needing to know array geometry
frontal = Va_prime; 
sagittal = permute(Va_prime,[2 3 1]);
horizontal = permute(Va_prime,[1 3 2]); 

% just pick which image to output
outpict = frontal; 
outpict = rot90(outpict,1); % just rotate the whole thing if necessary

folder='direction  file';
for p=1:size(outpict,3) % automatically picks the right number of slices
    outslice = outpict(:,:,p);
    
    % picking filenames and stuff
    basefilename=sprintf('image %d.png',i);
    fullfilemane=fullfile(folder,basefilename);
    imwrite(outslice,fullfilemane);
end

% you could put this in the loop, but it slows things way down
% and you'll only see the last slice anyway
imshow(outslice)

You'll have to check the orientation of the saggital/horizontal slicing with respect to your image. You can just swap them if they're flipped.

[Meriem YOUss]

The code is working, you solved my problem. Thanks so much for the help.