FW from http://openwetware.org/wiki/Beauchamp:ProcessDiffTensImgData

Notes on Eddy Current Correction

To reduce Eddy Currents, Phillips recommends increasing the partial k-space collected from 0.5 to 0.73; Vips does this as a matter of course. Phillips does not support the double spin-echo method described below, but YuXiang has implemented it and finds that it gives very similar results to the standard Phillips sequence. Note the importance of 12-parameter registration with 3dAllineate:

1. here, alignment of each DWI to skull stripped anatomy is done with the warp affine_general (12 parameter option)

3dAllineate -base {$ec}anatSS+orig -source {$ec}_DMaps+orig -prefix {$ec}DWIREGtoSSanat -verb -warp affine_general -EPI -cost mutualinfo -1Dfile {$ec}DWIREGtoSSanatXform -master {$ec}_DMaps+orig

1. compute the diffusion tensors; Daniel Glen says the –reweight option should provide additional help to reduce eddy current distortion

3dDWItoDT -prefix {$ec}_Tensors -automask -reweight -max_iter 10 -max_iter_rw 10 DWGradientVectorsAfter12-21-07.txt {$ec}DWIREGtoSSanat+orig'[0..32]'

Eddy-currents can be a problem, but there aren't that many reliable correction methods out there. The FSL method is just a matter of performing affine registration to the b=0 image, which isn't necessarily the best approach given that the b=0 image has a large CSF contribution, which is absent from the DW images - in certain cases, that's been shown to introduce 'over-stretching' of the DW images to fit the extra ring of CSF. That shouldn't however be a problem with your data, since they seem to have very good SNR.
In general, the most effective approach is to use the so-called 'twice-refocused' acquisition, which is designed to minimise eddy-current effects - it is effectively a double spin-echo sequence. Here's the reference if you need it:
Reese TG, Heid O, Weisskoff RM, Wedeen VJ Reduction of eddy-current-induced distortion in diffusion MRI using a twice-refocused spin echo Magn Reson Med 2003; 49 (1): 177-182
It is the default of Siemens systems, and has been for several years now. I can't tell from the DICOM data you sent me whether your data were acquired with a single or double spin-echo sequence, but I would be surprised if Philips didn't also at least offer that sequence. If your data were acquired with the twice-refocused sequence, then distortions due to eddy-currents should be negligible, or at least sub-voxel. If they were acquired with a single SE sequence, then you do unfortunately need to correct for eddy-currents.
However, what I noticed was that the DICOM data you sent me had a fair bit of motion artefact, which had obviously been corrected in the equivalent NIfTI image. Whatever routine you used to do the motion correction did a very good job, and the resulting images do not seem to have any significant eddy-current artefact in them - you can usually tell by looking at the colour-coded direction maps: with eddy-current artefacts, there's usually a ring of colour around the edges of the brain, where the various DW images don't match. It's possible that your motion correction also performs eddy-current correction as a by-product. This will be the case in particular if you used a full affine registration algorithm (i.e. 12 degrees of freedom, including scaling & shearing), rather than a simpler rigid-body algorithm (i.e. 6 degrees of freedom, only translation & rotation). For example, the eddy-correct routine in FSL uses such an affine registration routine, which explicitly allows scaling, shearing & translation (all possible consequences of eddy-current effects). You might want to check what algorithm you used for the motion correction, and in particular what parameters were used, as you may already be performing eddy-current correction...
Hope that helps,
Donald.