N4 Bias Field Correction

Overview

Code

Python

R

#!/usr/bin/env python

from __future__ import print_function

import SimpleITK as sitk
import sys
import os

if len ( sys.argv ) < 2:
    print( "Usage: N4BiasFieldCorrection inputImage " + \
        "outputImage [shrinkFactor] [maskImage] [numberOfIterations] " +\
        "[numberOfFittingLevels]" )
    sys.exit ( 1 )


inputImage = sitk.ReadImage( sys.argv[1] )

if len ( sys.argv ) > 4:
    maskImage = sitk.ReadImage( sys.argv[4] )
else:
    maskImage = sitk.OtsuThreshold( inputImage, 0, 1, 200 )

if len ( sys.argv ) > 3:
    inputImage = sitk.Shrink( inputImage, [ int(sys.argv[3]) ] * inputImage.GetDimension() )
    maskImage = sitk.Shrink( maskImage, [ int(sys.argv[3]) ] * inputImage.GetDimension() )

inputImage = sitk.Cast( inputImage, sitk.sitkFloat32 )

corrector = sitk.N4BiasFieldCorrectionImageFilter();

numberFittingLevels = 4

if len ( sys.argv ) > 6:
    numberFittingLevels = int( sys.argv[6] )

if len ( sys.argv ) > 5:
    corrector.SetMaximumNumberOfIterations( [ int( sys.argv[5] ) ] *numberFittingLevels  )


output = corrector.Execute( inputImage, maskImage )

sitk.WriteImage( output, sys.argv[2] )


if ( not "SITK_NOSHOW" in os.environ ):
    sitk.Show( output, "N4 Corrected" )

# Run with:
#
# Rscript --vanilla N4BiasFieldCorrection.R inputImage, outputImage, shrinkFactor, maskImage, numberOfIterations, numberOfFittingLevels
#

library(SimpleITK)

args <- commandArgs( TRUE )

if (length(args) < 2) {
    stop("At least 2 arguments expected - inputImage, outputImage, [shrinkFactor], ",
         "[maskImage], [numberOfIterations], [numberOfFittingLevels]")
}

inputImage <- ReadImage(args[[1]])

if (length( args ) > 4) {
    maskImage <- ReadImage( args[[4]] )
} else {
    maskImage <- OtsuThreshold( inputImage, 0, 1, 200 )
}

if (length( args ) > 3) {
    inputImage <- Shrink( inputImage, rep(strtoi(args[3]), inputImage$GetDimension()) )
    maskImage <- Shrink( maskImage, rep(strtoi(args[3]), inputImage$GetDimension()) )
}

inputImage <- Cast( inputImage, 'sitkFloat32' )

corrector <- N4BiasFieldCorrectionImageFilter()

numberFittingLevels <- 4

if (length ( args ) > 6) {
    numberFittingLevels <- strtoi( args[[6]] )
}

if (length ( args ) > 5) {
    corrector$SetMaximumNumberOfIterations( rep(strtoi( args[[5]], numberFittingLevels)) )
}

output <- corrector$Execute( inputImage, maskImage )

WriteImage(output, args[[2]])