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
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