Mask to feed into EDDY

[SabreA7]

Hi team,

I have successfully run Synb0 and am preparing to feed the data in EDDY. I was wondering in order to create a brain mask for EDDY, should I be using the Synb0 output for this? if so, which file?

Thank you for your help,

[hanscol]

The current Synb0 output does not include a brain mask. We do run bet to skullstrip the T1 image, but we don't save the mask itself. Anyways you would want a mask in the same space as your diffusion data not the T1. The easiest thing to do would be to use bet to get a mask using your topup corrected b0 image.

[SabreA7]

Brilliant, thank you so much for the advice.