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FSL  March 2009

FSL March 2009

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Subject:

Re: Donating scripts for rotating bvecs after ecc

From:

Matt Glasser <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 31 Mar 2009 15:11:12 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (112 lines)

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.  

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 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
much your 
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
it won't 
matter too much).

-Pablo

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.
>
>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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