Dear Burkhard,
We have not tried to optimise eddy_correct for this situation (limited FOV)
although I am surprised that it fails. You might want to try a different
cost function. If you take a copy of the file $FSLDIR/bin/eddy_correct
then you can modify the call to flirt (near the end) and try other cost
functions to see if they do better. Also check that your reference volume
is a good choice.
All the best,
Mark
On 3 Aug 2011, at 14:54, Burkhard Maedler wrote:
> Hi FSL-forum,
> I try to use eddy_correct on a subset of sagital DTI-data. Only the centre of the brain (main part of corpus callosum; 10 slices to either side) has been included.
> It looks "eddy_correct" has difficulties with handling the affine transformation of such a subset since it cannot perform a decent ECC for each gradient encoding.
> Some transformation matrices are completely screwed, e.g.
>
> regular (well behaved transform) matrix would look like this:
> Final result:
> 1.006631 -0.000593 0.000401 0.140801
> 0.002273 1.002451 -0.006194 0.016195
> -0.001417 -0.001287 1.008597 -0.137913
> 0.000000 0.000000 0.000000 1.000000
>
> but for some volumes (gradient orientations) I get matrices like this:
> Final result:
> 0.566810 0.150488 -0.212689 67.358504
> -0.107210 0.875570 -0.004303 8.674744
> 0.138302 0.020314 0.880910 22.970297
> 0.000000 0.000000 0.000000 1.000000
>
> which leads to completely useless results.
>
> I don't know why ECC is not able to correctly register the individual volumes. The susceptibility induced distortions
> between all volumes is minor and other registration software can perfectly handle this. When I also use a complete
> sagital set of data (60 slices accross the brain) this behaviour does not occur.
>
> Any help appreciated, as always.
>
> Burkhard.
>
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