MRIwrite Mask to NIfTI File

Hi MATLAB,

I have two MRI segmentation masks in NIfTI format (attached). I would like to subtract one mask (lesion) from another (wholebrain) and output a seperate NIfTI file of the result. So far I have the following, but I was wondering if anyone could please reccommend how to output the file per above using MRIwrite?

datadir = '';
d = dir([datadir filesep '*Lesion_Mask.nii.gz']);
    disp(['Found ' num2str(length(d)) ' Lesion Masks ' ]);
d = dir([datadir filesep '*Wholebrain_Mask.nii.gz']);
    disp(['Found ' num2str(length(d)) ' Wholebrain Masks ' ]);
resultspath = '';

Nd = numel(d);

for i = 1 : Nd
    disp(sprintf('Working on case %d of %d: %s',i,Nd,d(i).name))
    f = find(d(i).name=='_');
    prefix = d(i).name(1:f(1));  
    lesionmask = fullfile(datadir,[prefix '*Lesion_Mask.nii.gz']);
    wholebrainmask = fullfile(datadir,[prefix '*Wholebrain_Mask.nii.gz']);

    MMmri = MRIread(wholebrainmask); %read wholebrain mask
    LMmri = MRIread(lesionmask); % read lesion mask

    MMmri.vol(LMmri.vol>0)=0; % kill lesion mask
    
end

Answer 1

[Akshat]

Hi Annabel,

As per my understanding of the question, you want to perform some operations on MRI images present with you and write it to a file.

I searched the documentation and did not find any “MRIRead” or “MRIWrite” functions. On the other hand, there is a function to read NIfTI files and write them.

Here is the documentation of “niftiread” and “niftiwrite”, the functions I have used to read and write the files.

https://www.mathworks.com/help/images/ref/niftiread.html

https://www.mathworks.com/help/images/ref/niftiwrite.html

Hence, I have provided an updated code which is working for your inputs. Also, as of now, I have not done the “subtraction”, as it is not clear to me how to perform the subtraction. You can change the line number 20 in the code as you wish to and subtract the inputs.

datadir = '';
d = dir(['*Lesion_Mask.nii.gz']);
    disp(['Found ' num2str(length(d)) ' Lesion Masks ' ]);
d = dir(['*Wholebrain_Mask.nii.gz']);
    disp(['Found ' num2str(length(d)) ' Wholebrain Masks ' ]);
resultspath = '';

Nd = numel(d);

for i = 1 : Nd
    disp(sprintf('Working on case %d of %d: %s',i,Nd,d(i).name))
    f = find(d(i).name=='_');
    prefix = d(i).name(1:f(1));  
    lesionmask = fullfile(datadir,[prefix 'Lesion_Mask.nii.gz']);
    wholebrainmask = fullfile(datadir,[prefix 'Wholebrain_Mask.nii.gz']);

    MMmri = niftiread(wholebrainmask); %read wholebrain mask
    LMmri = niftiread(lesionmask); % read lesion mask
    
    subtractedMask = MMmri; %You can perform your subtraction here. 
    outputFilePath = fullfile(resultspath, [prefix 'Subtracted_Mask']);

    % Write the result to a NIfTI file
    niftiwrite(subtractedMask,outputFilePath,"Compressed",true);
    
end

Hope this helps!

Regards

Akshat Wadhwa