n4_bias_correction.py

from nipype.interfaces.ants import N4BiasFieldCorrection
import sys
import os
import ast

if len(sys.argv) < 2:
    print("INPUT from ipython: run n4_bias_correction input_image dimension n_iterations(optional, form:[n_1,n_2,n_3,n_4]) output_image(optional)")
    sys.exit(1)

# if output_image is given
if len(sys.argv) > 3:
    n4 = N4BiasFieldCorrection(output_image=sys.argv[4])
else:
    n4 = N4BiasFieldCorrection()

# dimension of input image, input image
n4.inputs.dimension = int(sys.argv[2])
n4.inputs.input_image = sys.argv[1]

# if n_dinesions arg given
if len(sys.argv) > 2:
    n4.inputs.n_iterations = ast.literal_eval(sys.argv[3])

n4.run()