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I have a large dataset of nifti scans, and each scan has a corresponding tumor segmentation mask also as a nifti file.

There is also a brain stripping mask which is for the entire dataset.

How can I use numpy or nilearn to use the brain stripping mask to 'remove' or set all pixels not in the mask to 0? How can I also use numpy to enhance / brighten those areas on the original scan where the segmentation mask is indicating a tumor?

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    Can you provide some starter code and image examples? – rikyeah Apr 19 '22 at 08:01
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    The question is a bit too open ended to fit this Q&A forum. Please add some example code or image etc to show what direction you started, and why that didnt work. – LudvigH Apr 19 '22 at 08:11

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