The difficulty with fMRI data is that there is signal loss and this is not modelled within eddy at the moment. This is something that is being looked into for future versions of eddy, but at the moment we do not know how well it will work on most fMRI data. It is something that you could try and carefully evaluate on your data in comparison with other motion correction methods.
All the best,
> On 25 Aug 2017, at 18:31, John anderson <[log in to unmask]> wrote:
> Hi FSL experts,
> Can I use eddy current correction tool to correct motion in bold fMRI data. My understanding is that eddy splits the volume and then register them to a reference volume. We do this in DTI. Is it OK to use it for fMRI to derive motion parameters and correct for motion?
> Thanks in advance