Dear fsl-ers, I’m aligning two different T2 images from a single subject, each of which has its own manually drawn ROI, and need advice on how to improve alignment. Using tri-linear interpolation gives good registration but of course blurs the ROI. Nearest neighbor keeps the ROI’s integrity but changes the T2 non-uniformly, e.g., changing the pitch of the anterior 2/3 of the image while separately effectively moving the occipital lobe superiorly. Skull stripping does not help. Any advice on the best way to address this within FSL would be great. Thanks, Chris
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