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skull_stripping.py
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skull_stripping.py
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'''
Created on 21 de fev de 2017
@author: Alexandre Yukio Yamashita
'''
import ntpath
import os.path
from shutil import move
import os
def skull_strip(input_path, output_path):
'''
Extract brain removing skull and muscular tissues.
'''
try:
# Get filename and extension from input path.
basename = ntpath.basename(input_path)
extension = os.path.splitext(basename)[1]
input_path = os.path.abspath(input_path)
if extension == ".gz":
extension = ".nii.gz"
filename = basename.replace(extension, "")
dir_path = input_path.replace(basename, "")
# Extract brain.
command_txt = os.getenv('FSLDIR').rstrip() + "/bin/bet " + \
dir_path + filename + " " + \
dir_path + filename + "_brain" + \
" -R -f 0.5 -g 0"
print command_txt
os.system(command_txt)
move(dir_path + "/" + filename + "_brain" + extension, output_path)
except:
print "Error in extracting brain from " + input_path
if __name__ == "__main__":
'''
Skull stripping.
'''
input_path = 'resources/sample.nii.gz'
output_path = ''
# Skull strip image.
skull_strip(input_path, "resources/sample_brain.nii.gz")