Normalise segmentations to MNI space

Hello all. I have a couple hundred MRI scans of patients with brain metastases which have been segmented. I want to create a heat map of all the lesions. I can normalise the individual MRI scans to MNI space using SPM12, is there a way to also normalise the segmentations? I can then use MRIcron to create a heat map. Or if there are any other suggestions on how to create a heat map within 3Dslicer?

Many thanks for your help.

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