This simple program is based on SimpleITK and performs N4 bias field correction on a 3D volume.

• SimpleITK

For a 3D volume saved as a NIfTI file ./input.nii, the following script saves the bias field corrected volume as a NIfTI file ./output.nii whose filename is specified by --output or -o.

python N4.py -i ./input.nii -o ./output.nii

A mask can be specified using --mask_file or -m. If unspecified, a mask will be automatically generated using Otsu's method. Note the specified mask should be of the same shape as the input volume.

To specify the number of iterations to perform, use --iterations or -n. More iterations yield better result but also takes longer to run. The default number of iterations is 50.

Use --get_bias_field or -b to save the estimated bias field as a NIfTI file under the same directory as the output file.

Use --get_mask or -k to save the generated/specified mask as a NIfTI file under the same directory as the output file.

To enable progress reporting, use --verbose or -v (only works with SimpleITK 2.3.0 or later). To install the latest pre-release version of SimpleITK, run the following command in a terminal:

pip install --upgrade --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/latest