Thanks heaps for the quick reply.
I used the mrtrix pipeline from mrconvert to dwibiascorrect starting directly from the dicoms. I am using 3.0_RC3. I have noticed the version being missing from the header. Not sure if it’s because prior versions of MRtrix are also available (I am running MRtrix in a cluster, but 3.0_RC3 is the default).
The simple solution is to allow dwibiascorrect to generate its own mask but then again, this does not work in some cases where ANTs fails the same as in this and this posts. So this issue is also happening with 3.0_RC3, but I know the parameters can be adjusted with the -ants options in dwibiascorrect as a way to address this. Unless it is advisable to change the header of the mask passed to dwibiascorrect so that is has the same origin as the input?
I’d say this was the case as the header changes from the input to dwipreproc to its output.