Hi MRtrix experts,
I want to preprocess a dataset acquired with a HCP-style protocol using mrtrix tools. I have 4 images per subject with 99 and 98 gradient directions acquired in AP and PA.
Currently, I am running dwidenoise and mrdegibbs on each of these four images separately, and then concatenating gradient and phase encoding directions to end up with a single image that has its first half of volumes in AP and the remaining in PA. After this, I pass this image to dwifslpreproc for topup, motion, and eddy.
Is this an appropriate workflow for handling this kind of dataset? And if so, can I then proceed to use dwibiascorrect on the resulting image and mtnormalise on FODs, or would they produce suboptimal results due to the multiple image concatanations that I am performing?
Best,
Ozzy