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Do you see stretching when there is no mask at all? I think I had a similar problem to yours in the thread titled "applywarp and ApplyXFM produce different output". On Tuesday, December 06, 2011 22:48:24 you wrote: > 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