How to register nifty image and corresponding segmentation mask into MNI152 space?

I would like preprocess mri images and labels (t1,t2, flair modalities) and register all of them into mni152 space using the FSL. Looks like images could be processed by “flirt” utility but how process binary masks?

Hi, if your binary mask is in the same space as, say, the T1w image, you should be able to apply the transform you calculated to register the T1w image to the mni152 space to the binary mask. I would guess it would be best to use -interp nearestneighbour as interpolation procedure and to binarize the resulting image with fslmaths afterwards:

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