How to combine multiple ROI masks (.nii files) into one .nii file

HI

How to combine multiple ROI masks (.nii files) into one .nii file?

for example, if I have the right amygdala.nii and left amygdala.nii, how can I combine them into amygdala with both sides?

furthermore, if I have the right, left, anterior and posterior side of insula, how can I combine them into one file as insula?

I've tried the script below,

but while I check the "add overlay function" with MRIcroGL, there's nothing:

clear all;

clc;

ROIFolder=['D:\000ROIMask\AMG'];

cd(ROIFolder);

% ROIFolder=fullfile(pwd, '\functional');

files=dir(fullfile(ROIFolder, '*.nii'));

fileNames={files.name};

for k = 1:numel(fileNames)

fname = fullfile(ROIFolder, fileNames{k});

z(k) = load_nii(fname);

y(:,:,:,k) = z(k).img;

end

% Create the ND Nifti file

output = make_nii(y);

% Save it to a file

save_nii(output, 'myfile.nii')

Thank you so much for your help...

Rainbow

Answer 1

[Sarthak]

Hi Chia-Yueh Chang,

As per my understanding your approach seems correct. However, you are not specifying the combined ROI mask using any logical operations, which could be the reason why you are not seeing any overlay when checking with MRIcroGL.

To combine the multiple ROI masks into one mask, you need to use logical operations (e.g., or, and, etc.) on the voxel values of the loaded .nii files.

After loading your files, you may modify your code as

% Combine the ROI masks using logical OR operation along the 4th dimension 
combined_mask = any(y, 4);  
% Create a new NIfTI structure for the combined mask  
output = make_nii(combined_mask);  
% Save the combined mask as a new .nii file  
save_nii(output, 'myfile.nii'); 

Please note that the resulting combined mask may need to be thresholded or processed further depending on your specific use case and requirements.

Attaching some documentation for your reference

https://www.mathworks.com/help/matlab/ref/any.html

https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image