Hey @jingleil,
Just a small warning on this topic: while it might appear mtnormalise compensates a bit for gradient non-linearity effects, it’s not the appropriate way to deal with these, or a solution to it generally speaking. If you use the minimally preprocessed HCP data, I’d advise to practice caution when performing experiments that rely on absolute intensities being comparable across/between different brain regions or tracts within subjects. This even more so when using large numbers of subjects: due to the high quality and large numbers of subjects available in the HCP dataset, there is a realistic chance of pulling out even small effects. I still recommend to run mtnormalise regardless on the HCP data, at least for the other intensity inhomogeneities in this dataset. Just don’t expect it to correct the effects of gradient non-linearities.
Cheers & take care,
Thijs