Hello all,
I wanted to check what the going recommendations were with respect to running any needed motion correction on the fieldmap images.
More concretely: I'd like to align the magnitude and phase images -- both of which were acquired at the end of a scan session -- to the initial functional volume, which had been acquired about 40 minutes prior.
In my discussions with others in this situation, two specific areas of uncertainty came up. First, is it advisable to request a specific cost function when using flirt to align a fieldmap magnitude image to a functional volume (due to the differing contrast)? Second, when the transformations are applied to the magnitude and phase images, is there any argument for using a different interpolation scheme than the default trilinear approach?
I understand that there may not be any good way to know a priori what will work best, in which case I'm happy to just proceed with the trial-and-error process and see how things go.
Thanks much --
Karin
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