Hi MRTrix experts,
I learned that the order of the DWI correction is dwipreproc to dwicorrectbias.
But I don’t understand why this order is.
Why is the order of corrections not in the reverse order?
I want to know why we have to correct in this order(dwipreproc→dwibiascorrect).
I’m looking forward to hearing the answer.
The script to do bias fueld corrections, estimates the bias fueld fron the average B0 image and then it applies it ti the rest of the volumes, so it is necessary that your volumes are correctly aligned. This is why this step should be performed after dwipreproc (dwirpeproc runa eddy and is in charge of aligning the volumes).
Bias field correction also relies on a good brain mask, which tends to be easier after
dwipreproc rather than before. Then again, internally
dwipreproc also requires a brain mask; so it’s a circular problem. Ideally it would be a single iterative process to estimate and correct all of these non-ideal image attributes, but we have to work with the tools we have available right now.
There’s nothing stopping you from experimenting with the orders of commands: we prefer to expose the underlying commands and let people do with them as they wish, rather than having a single opaque “do all” command.