Yep - sure, but you will need to turn your new bmatrices into bvectors.
Bedpost does not allow b-matrices as inputs (thus making
the assumption that the imaging gradients have a small diffusion encoding
effect in comparison with the diffusion encoding gradients).
Cheers
T
On Wed, 29 Jun 2005, Marenco, Stefano (NIH/NIMH) wrote:
> We run a program that does the eddy corrections, realignment for motion, abd
> rigid body alignment in Talairach space, but outputs a recalculated
> b-matrix.
> Would it be possible to use our rotated b-matrix as the input for bedpost
> rather than the original gradient directions and bvalues?
>
> Stefano Marenco, MD
> GCAP, Clinical Brain Disorders Branch,
> NIMH
> 10 Center Drive, room 4S235
> Bethesda, MD 20892
> tel. (301) 435-8964
> fax. (301) 480-7795
> email: [log in to unmask]
>
>
> -----Original Message-----
> From: Tim Behrens [mailto:[log in to unmask]]
> Sent: Monday, June 27, 2005 10:31 AM
> To: [log in to unmask]
> Subject: Re: [FSL] eddy_correct, head rotations and gradient directions
>
> Dear Stefano -
>
> The output matrices are stored in the ecc_log so that the
> conscientious user may choose to rotate the bmatrices accordingly.
> However, my experiences are that rotations large enough to have a
> noticeable affect on the relative orientation between gradient and image
> axes, will also cause much more obvious corruptions to the data!!
>
> You can minimize the effect of head motion on the recovered principal
> diffusion direction by clever sampling of your gradient directions.
> Importantly you should make sure that similar directions are not all
> sampled at close timepoints in the scan.
>
> T
>
>
>
>
> On Mon, 27 Jun 2005, Marenco, Stefano (NIH/NIMH) wrote:
>
> > I was wondering about eddy_correct. According to the website, the program
> > realigns the images with an affine transform to one of the volumes and in
> > doing this corrects for motion and eddy current distortion. Does this
> > program rotate volumes to align them with each other? If so, how does it
> > keep into account the rotation of the b-matrix relative to the frame of
> > reference of the head?
> >
> >
> >
> > Stefano Marenco, MD
> >
> > GCAP, Clinical Brain Disorders Branch,
> >
> > NIMH
> >
> > 10 Center Drive, room 4S235
> >
> > Bethesda, MD 20892
> >
> > tel. (301) 435-8964
> >
> > fax. (301) 480-7795
> >
> > email: <mailto:[log in to unmask]> [log in to unmask]
> >
> >
> >
> >
>
>
--
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Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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