Advanced Normalization Tools (ANTs) is a powerful set of tools used for registration, template creation, brain morphology, region of interest extraction, thickness extraction and comparison, and so forth. More examples of its use are here.

Installation

Rather than reproduce the install method here, please visit the ANTs GitHub Wiki for installation instructions. Any issues can be addressed to the developers.

Bias field correction

Correcting the bias field can be time consuming on the computer, although the following runs in about one minute on a fast, modern laptop. One way to mitigate the computer processing time is to run the program several times on the same image from starting very coarse and moving in more finely:

$ N4BiasFieldCorrection -d 3 -i ~/preprocessing-t1-example/1222_032309/acpc.nii -o ~/preprocessing-t1-example/1222_032309/n4.nii.gz -s 8 -b [200] -c [50x50x50x50,0.000001]
$ N4BiasFieldCorrection -d 3 -i ~/preprocessing-t1-example/1222_032309/n4.nii.gz -o ~/preprocessing-t1-example/1222_032309/n4.nii.gz -s 4 -b [200] -c [50x50x50x50,0.000001]
$ N4BiasFieldCorrection -d 3 -i ~/preprocessing-t1-example/1222_032309/n4.nii.gz -o ~/preprocessing-t1-example/1222_032309/n4.nii.gz -s 2 -b [200] -c [50x50x50x50,0.000001]