overlay nifti mask on nifti volume
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i have a 3d MRI in nifti format and a 3d binary mask in nifti. how to overlay the mask on the volume and eliminate the undesired regions?
NOTE: I want to apply glcm on the result.
Mask:
![](https://www.mathworks.com/matlabcentral/answers/uploaded_files/610925/image.png)
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Asvin Kumar
il 10 Mag 2021
Once imported, it behaves just like any 3D matrix. You can then apply your 3D binary mask on that data.
Here's an example of processing NIfTI data that applies a 3D median filter on the imported volume: Write Median-Filtered Volume to NIfTI File This example should give you an idea of what you can do.
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Asvin Kumar
il 11 Mag 2021
I'm not a 100% sure about how MRI data is represented. Since you mention that you want to apply GLCM on this masked MRI, I assume, that the lowest value for MRI voxels is 0 and that stands for 'low'. You can adjust this as required.
If you had a 3D matrix, here's how you could apply a binary mask.
vol = randi(10,[4 4 6]) % similar to original MRI data
mask = vol>7; % creating my own binary mask
maskedVol = vol;
maskedVol(~mask)=0 % setting to 0 if values of voxel is not >7
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