I’m new to MRtrix and I have a few questions about preprocessing before eddy correction.
1- I’m aware that dwidenoise should be the initial preprocessing step before anything else. But how should my dwi data be organized? Currently my dwi.nii.gz consists of an image with no diffusion every 8 images with diffusion. Can I simply feed dwi.nii.gz to dwidenoise? Shouldn’t I specify bvals somewhere?
2- I assume that B1 field inhomogeneity and Gibbs artifact are not corrected with dwidenoise. Can I still apply dwibiascorrect and mrdegibbs after dwidenoise (but before eddy correction)?
3- are there any other preprocessing steps you would recommend before running eddy?