Dear Matthew,
In FSL5 we initially register the non-distorted fieldmap to the non-distorted structural image, avoiding the problems of going to the distorted functional space that existed in FSL4.x. We get much better results with the BBR method implemented in FSL5 and I would strongly encourage you to upgrade to this in order to take advantage of that. It should fix all these problems for you.
All the best,
Mark
On 3 Oct 2012, at 18:30, Matthew Ward <[log in to unmask]> wrote:
> Hello. In regard to FUGUE unwaping, is there a way to constrain the search it performs to put the non-distorted fieldmap into functional space? Such as rigid body? Due to some dropout/warping in the functional image, there is an erroneous rotation being applied along the Z-axis that is putting them out of alignment. Also, what is the default search that is used for functional/fieldmap alignment in FUGUE? Any thoughts would be most appreciated. Thanks!
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> Matthew
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