Dear Alex,
>
> What brain mask should I create a brain mask for Eddy if there is movement in the DTI sequence?
> I am using BET on the first b=0 volume, is this correct? Even if is doesn't fully match the brain position in some of the other volumes?
yes, that is correct. The mask is only used for selecting voxels for the estimation of the hyperparameters, so isn’t very critical. Note also that it is better with a too conservative (small) mask than a too big.
Jesper
>
> Thanks.
>
> Best,
> Alex
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