Given that the bias field estimated within
dwibiascorrect ants by
N4BiasFieldCorrection is spatially smooth by construction, and all
dwibiascorrection ants does is a division operation of the DWI data against such, I unfortunately have no choice but to attribute the anatomical contrast present in those images to … user error (Sorry!)
Normally I’d ask for the exact sequence of commands that were used to generate the images shown; in this case I’m hoping that, by going through the process of trying to produce such in order to prove me wrong, you’ll figure out what’s gone wrong. You can also use the
-bias option for
dwibiascorrect ants to export the estimated bias field directly, which might help to hone in on the discrepancy.
We can see that the residual bias field maps in AP and PA directions is not the same. Would it make more sense (in this case) to perform bias correction before eddy correction?
I’d want to both resolve the first point, and interrogate potential sources of the discrepancy, first before making a decision on the processing pipeline.
Assuming that you’ve not changed the head coil between the two phase encoding directions, potential sources of such variation in bias field are:
Massive change in patient position within a parallel coil set;
Fundamental instability in the scanner’s internal calibration;
Different parameters between the two sequences (e.g. using Siemens’ “Prescan Normalise” for one but not the other, or using a parallel receive coil for one and body coil for the other);
Fundamental instability in N4’s estimation process (i.e. the actual bias field is in fact comparable between the two series, but its estimation of such is wrong).
Since none of these are of particularly high likelihood, I would encourage you to interrogate further.