Hi Franck,
I haven't found a hint in your e-mail which image volume you specify as
reference image.
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
