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Hi - No eddy_correct does not align the vectors for you - however it does output the list of reorienting matrices (ecc.log), so it would be easy for you to reorient them for themselves. All the studies I have seen suggest that this will make very little difference unless motion is big, and is motion is big you probably have far worse problems anyway!! T On 3 Sep 2007, at 05:07, Andrew Z wrote: > I have a query about the eddy current correction scheme in FSL. > > As part of eddy current correction, my understanding is that each > diffusion-weighted volume is linearly aligned to a reference > volume, where > the reference volume is typically chosen as an average over all the > b=0 > volumes acquired. > > In aligning a d-w volume to the ref vol, it seems we also need to > re-align > the gradient vectors accordingly. In particular, the gradient vectors > should be re-aligned according to the matrix taking d_w to ref. > Given that > the d_w to ref matrix is not necessarily unique across all d-w > volumes, it > also seems each d-w volume has its own unique set of re-aligned > gradient > vectors. Specifically, a common set of gradient vectors cannot be > assigned > to all d-w volumes. > > Does the eddy current correction scheme in FSL perform re-alignment > of the > gradient vectors? My guess is that this kind of re-alignment is not > really > a big deal so it has not been implemented. > > Andrew