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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