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.
