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Dear Luca,

The swmc1 files are obviously skull-stripped, so they should indeed look similar to each other. It does not matter whether the field of view for the T1 image of a certain subject was shifted somewhat more dorsally or ventrally as long as the brain was covered. This would not necessarily be the case for e.g. fMRI data with a limited number of slices and possibly also holds for the PET images. Depending on original FOV you would have non-zero voxels in more ventral slices in the normalised data of some subjects but not in others simply because these regions were covered in only some of them.

Hopefully this explains your findings. Otherwise it might be useful if you could upload some screenshots somewhere to get a visual impression of your issue.

Best regards

Helmut