Query on running EDDY after synb0

[george-gifford]

Hi there,

When you run eddy after synb0, e.g.

eddy --imain=path/to/diffusiondata.nii.gz --mask=path/to/brainmask.nii.gz \ --acqp=path/to/acqparams.txt --index=path/to/index.txt \ --bvecs=path/to/bvecs.txt --bvals=path/to/bvals.txt --topup=path/to/OUTPUTS/topup --out=eddy_unwarped_images

Is --imain=path/to/diffusiondata.nii.gz the orginal distorted file and --mask=path/to/brainmask.nii.gz a brain mask that is computed on the undistorted b0?

Or should --imain=path/to/diffusiondata.nii.gz be undisorted?

Many thanks for any advice! George

[schillkg]

Hi George - yes, it should point to the original, raw diffusion data, and the brain mask is indeed a mask. The mask doesn't need to be perfect at this stage - FSL recommends running BET command on the topup output (topup_iout.nii.gz, or similar) (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#A--mask).

[george-gifford]

Many thanks OK!