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Hi Mark,

Thanks for the clarification. But my question is why those two options are
used in eddy_correction. --- Are those options used to improve the
estimation of the diffusion tensor parameters? --- I find that some people
use the default flirt command without using any options to preprocess the
DTI scans so I tried that way  and found that the estimated FA maps are
different from the one using eddy_correct. So I wonder which method should
I use.

Best,
Leo


On Tue, Apr 3, 2012 at 6:50 AM, Mark Jenkinson <[log in to unmask]> wrote:

> Dear Leo,
>
> The -nosearch is to stop an *extensive* initial search of rotation angles.
> It does not the optimisation method from finding non-zero rotations, and
> you will find that it does in fact correct for rotations.
>
> The -paddingsize is to make sure that end slices are not lost due to small,
> half-voxel shifts of the FOV.  This just copies the intensities from the
> nearest end slice into any areas which have fallen outside the original FOV
> by up to 1 voxel.
>
> All the best,
>        Mark
>
>
>
>
> On 2 Apr 2012, at 23:27, Yiou Li wrote:
>
> > Dear FSL experts,
> >
> > Could you please advise the reason of using the -nosearch and
> -paddingsize 1 in the flirt command in eddy_correct?
> >
> > It seems to me that -nosearch constrains (or turn off?) the rotation in
> registration transformation -- is this because rotation transfomation could
> introduce artifacts in estimation of diffusion parameters?
> >
> > Thanks in advance!
> > Leo
> >
> >
>