Dear Anders,
> what is the most common way to correct for head motion in DTI data? To use the function eddy_correct?
>
> If I only want to do motion correction and no eddy correction (assuming it has already been done using some other function), should I then use flirt? mcflirt?
>
> Has there been any comparison of DTI motion correction tools, especially for high b-values?
there is a paper coming out soon (I think) from the UCL (Mark Graham el al.) group comparing eddy_correct and eddy. They also present a simulation framework that will hopefully facilitate more comparisons of eddy current/subject motion correction methods in the future.
I don’t want to reveal too much of their findings prematurely, but they find that eddy_correct performs worse than eddy. The strategy of eddy_correct, i.e. to use an affine transform and a cost-function that is “more accepting of differences in contrast”, is similar to some other methods of motion correction of diffusion data so it is likely that their conclusions extend to some of those. Though it remains to be proven of course.
My recommendation would be to use eddy if your data is such that it allows for it. In principle it should be fine with data that has already been corrected for eddy currents, but it depends on what that method does to the edges of the FOV. My personal preference would be to just use eddy to correct for both effects. Just out of interest, what method are you using for the eddy currents.
Good luck Jesper
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