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
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