You are correct: the diffusion gradients are applied in the undistorted space, so correcting
for the EPI distortions brings the images into "alignment" with the actual directions along
which the diffusion gradient were applied. However, the problem is that eddy_correct not
only corrects for eddy-currents and other EPI-related image distortions, but also for
subject motion. It is the actual physical rotation of the head what calls for a rotation of
the gradient directions, and there is no way to separate both effects (image distortions
and rigid-body rotations) in eddy_correct.
On Tue, 31 Mar 2009 11:01:49 -0500, Matt Glasser <[log in to unmask]> wrote:
>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.
>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
>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.