I am trying to register an epi to an anatomy using flirt to get better alignment. The anatomy has
been skull-stripped. The anatomy is 256X256X134, with 0.81x0.81x1.0 mm voxels. The epi is
64x64x36, with 3.25x3.25x3.30 mm voxels. Seems that flirt always wants to push the epi down (in
z direction, ventrally). I have tried various things, inlcluding chopping off the bottom parts of
anatomy and/or the epi. This happens with a number of subjects. Typically the epi is 2-3mm too
high, and is pushed down by 5-6 mm, making it too low. I have also tried all cost functions, and
tried reducing the 'finesearch' value to 6 and 8 from 18. Any help would be appriciated. I can send
an anat and an epi if necessary. Thanks!
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