Ah, I see the difficulty. Presumably one could run a 6 parameter motion
correction step, apply all angular transforms to the gradient table, and
then a 12 parameter eddy current correction where no transforms are applied
(my understanding of eddy currents is that they are mostly global image
skews and scales, or translations)? Unfortunately such processing would
take 2x as long and still probably not make any difference in the end.
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 12:03 PM
To: [log in to unmask]
Subject: Re: [FSL] Donating scripts for rotating bvecs after ecc
Hi Matt,
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.
-Pablo
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.
>
>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
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