ANTs bias correction

1

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. https://mrtrix.readthedocs.io/en/latest/reference/commands/dwibiascorrect.html

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!

Greetings,
Chris

2

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.

Cheers,
Max

3

Dear Max,

Thanks for your reply and the clarifications.

Greetings,
Chris