Hi - we've tried various tweaks and indeed the apparent motion, which
is minimal in the original data, always gets very slightly worse
after motion correction. It doesn't get particularly bad, but I
suspect that in this data it is better to just use the uncorrected
original data. Sorry we can't help more!
Cheers, Steve
On 10 May 2007, at 10:13, Lamberton Franck wrote:
> Hi,
>
> I worked with DTI a few weeks ago and used FDT in order to compute
> FA (last
> version of FSL running on Linux FC4).
> Recently, I acquired a set of diffusion weigthed images on a
> subject with
> minimal head movement (head control) :
> 40 slices
> 1 b=0 s/mm2 + 32 different encoding directions at b=1000 s/mm2
> resolution = 2x2x2 mm3
>
> Using the 'Movie mode' of fslview shows that very little distortion
> occured
> between successive acquisitions (they seem to be related to eddy-
> currents).
> After applying 'eddy_correct', significant geometrical distortion
> appeared
> in the se ries that were not present in the first place.
> I also used avwmaths++ command with the option -Tstd in order to
> compute the
> standard deviation of the series. Signifi cant geometrical distortion
> introduced by eddy_correct induced high std values all arround the
> brain.
>
> I edited the script 'eddy_correct' in order to test different
> options of
> FLIRT, cost function (-searchcost) and no ang ular research limitation
> (-nosearch).
> In all cases, spurious geometrical distortions remain the same after
> applying the modified 'eddy_correct'.
>
> I also used the option "-interp nearestneighbour" in order to
> better compare
> uncorrected and corrected series (less blurring). To do this, I used
> 'avwmaths++' with '-Tstd' option in order to compute the std volume
> of only
> corrected diffusion weighetd volumes. After correction, greater values
> appear at the periphery of the brain.
>
> Does anyone have already seen a similar effect of 'eddy_correct' ?
> What about using -refweight or -inweight of FLIRT ? How can I use
> this two
> options ?
>
> Thanks for any response
>
> Franck
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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