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Tim has told me in the past that the diffusion gradients are applied in undistorted space, and thus when you correct for EPI distortions you are actually making the data fit the applied gradients better. Not sure if that applies in this situation, but it would seem to. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Pablo Velasco Sent: Tuesday, March 31, 2009 4:57 AM To: [log in to unmask] Subject: Re: [FSL] Donating scripts for rotating bvecs after ecc Dear Martin, If the subject moves, rotating the bvecs is the correct thing to do, since the rotated directions are those along which the diffusion encoding gradients were actually applied. In that sense, it can't hurt you. However, eddy_correct doesn't correct just for motion, but also for eddy-current image distortions. The distortion correction is an image artifact, not actual motion, so the diffusion gradients will still be acting along the same direction with respect to the subject's brain. Therefore, you should only be correcting the bvecs for the motion component. Unfortunately, eddy_correct doesn't distinguish between them, so it is impossible to differentiate. Best, -Pablo Thinking of a situation where the rotation could hurt you On Mon, 30 Mar 2009 09:42:27 +0200, Martin Kavec <[log in to unmask]> wrote: >Thanks, Matt and Steve, > >could you suggest any tough tracking test to see whether it makes any >difference? Fornix is rather small and thin, so it may show some trackability >difference. > >Could you think of a situation, where the rotation of the bvecs could have an >adverse effect? I though it shouldn't hurt to use it in all the analysis. We >may not be able to see any difference in a major tracts, but maybe for some >fibers with multiple fibres in a voxel, or higher probability in a >subcortical projections, ... > >Best, > >Martin