Dear Mahmoud,

But we should provide a mask for eddy as for the option --mask, right?

yes, but that is only used to select a subset of voxels from which to estimate the hyperparameters of the Gaussian Process (internal prediction maker). All other things (estimation of eddy currents, movement etc) is based on all voxels.

Jesper

Thanks,

Mahmoud

On Thu, Jul 20, 2017 at 12:52 PM, Jesper Andersson <[log in to unmask]uk> wrote:

Dear Chelsea,

it is actually important that you _dont_ run bet before eddy. Eddy expects to get the data before any other processing has taken place.

Jesper


> On 19 Jul 2017, at 17:52, Chelsea <[log in to unmask]> wrote:
>
> I was wondering if it is important to run bet before running eddy.
>
> Thank you.