I have an EPI data set that I'd like to register to a FSE T2-weighted data set. Both are
T2-weighted images, with similar contrast characteristics, and both have the same
resolution (256x256 in-plane, 16 slices). The patient moved only a little between the EPI
and FSE acquisitions. The main problem is that the EPI data are slightly distorted,
basically just a little compressed in the phase-encoding (i.e. anterior-posterior)
dimension.
I don't have a B0 map, so I can't use FUGUE to correct this distortion. What kind of
results can I expect from trying to use FLIRT to correct the distortion and do a little
motion correction at the same time? It seems to me that, as the distortion is mostly just
a matter of scaling and translation in the AP dimension, I should be able to get pretty
good (if not perfect) results from an affine transformation. But I've been disappointed
with what I have tried so far.
Can anyone suggest optimum settings to use for FLIRT in this situation? Is there a way
that I can constrain FLIRT's fit so that translation and rotation are allowed in all three
dimensions, but scaling is allowed only in the Y dimension?
Thanks in advance,
William Copen, MD
Massachusetts General Hospital
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