ANTs bias correction

Dear all,

According to the ANTs documentation, you can specify the amount of dimensions on which ANTs is performed. As DWI is 4-dimensional, it is of course logical to use “-d 4”. However, in the MRtrix pipeline, i can not find the option of specifying this with dwibiascorrect.

Also, when I check the processing of ANTs bias correction with dwibiascorrect, I see the following: Command: N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0]

Would this mean that the bias correction is only performed on 3 dimensions, due to “-d 3”? And if so, would it then be better to do the ANTs bias correction outside of MRtrix, to be able to specify the dimensions?

Thanks for your help!


The bias field correction is 3D as the sensitivity profile of the receive coil is commonly assumed constant and not affected by the diffusion sequence.* dwibiascorrect passes the mean b0 image to ANTs N4, so changing dimensionality would not make sense even if the dimensionality parameter was included in the ANTs parameters.

If you use a multi-tissue pipeline, consider using mtnormalise additionally or instead of dwibiascorrect.


Dear Max,

Thanks for your reply and the clarifications.