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I am running very standard flirt & fnirt commands (as described on the fnirt webpage) to register T1 MPRAGE to the MNI152_T1_2mm template. I used skull-stripped images for flirt & non-betted images for fnirt, as suggested. I have noticed in some subjects there is quite a bit of stretching around the edges of the brain. This occurs to varying degrees in my subjects, and is most noticeable at the top of the brain and bottom of the temporal lobes (so in the z direction). I have seen other people post what sound like similar problems, with not much resolution. I serendipitously realized today that this problem seems to go away (at least in the subjects I've test so far) if I use the undilated (MNI152_T1_2mm_brain_mask) instead of the default dilated one (MNI152_T1_2mm_brain_mask_dil). Since the distortion is gone when I use the undilated mask I am inclined to use it for all subjects. Is there some reason that this is ill-advised? And along the same lines, why is the dilated mask chosen as the default to begin with? Thanks for any insight! Katy Cross UCLA