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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