Thanks a lot for your response
Jochen Hirsch a écrit :
> Hi Franck,
>
> I haven't found a hint in your e-mail which image volume you specify as
> reference image.
>
I used the following command :
eddy_correct input_colume_4D output_volume_4D 0
So, I use the b0-volume as a reference.
I understand that the high CSF signal can lead to wrong corrections. I
have already noticed that the external edge of the brain in
b1000-volumes (and thus, edge of the white matter) are moved toward the
edge of the CSF in b0-volume (and thus, edge of CSF).
Do you suggest to use another dedicated acquisition, with the same
parameters as the b0-volume but with an additional pre-inversion in
order to suppress signal from CSF ?
Or maybe using the mean volume of all b1000-volumes as a reference...
> But correction for eddy currents distortions will probably fail if you
> choose the b0-volume due to the high CSF signal which is not present in
> b1000-images.
>
> Regards,
> Jochen
>
>
>
>
>>>> Lamberton Franck <[log in to unmask]> 10.05.07 11.13 Uhr >>>
>>>>
> 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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