It is, of course, always prudent to evaluate the output of the eddy_correct
script, I too have seen situations where it makes things worse.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Pablo Velasco
Sent: Tuesday, March 31, 2009 1:18 PM
To: [log in to unmask]
Subject: Re: [FSL] Donating scripts for rotating bvecs after ecc
Yes, Matt: in principle you could try to do a first pass with 6 parameters
and apply those
rotations to the gradient directions. The problem I see with it is that
since the SNR of the
diffusion-weighted images is so low, and the contrast is so different from
the b=0 image,
you would have to make sure the motion correction does the right thing
(i.e., I wouldn't
just script it and think that it will do the right thing).
Regarding whether or not it will make a difference or not, it depends on how
subject moved: I would bet that if your subject tipped his/her head a few
degrees, it will
make a significant difference in the fibertracking results (maybe for the FA
matter too much).
On Tue, 31 Mar 2009 12:45:28 -0500, Matt Glasser <[log in to unmask]> wrote:
>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.
>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
>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
>which the diffusion gradient were applied. However, the problem is that
>only corrects for eddy-currents and other EPI-related image distortions,
>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
>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
>>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
>>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.