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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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Mask to feed into EDDY #20

Open SabreA7 opened 3 years ago

SabreA7 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

Brilliant, thank you so much for the advice.