bet - the main command-line script which makes calling the core bet2 and betsurf programs easy. BET is a function in FSL Tool

To batch extrain brain, we use command-line script wrote in Python as follows:

   bet <input> <output> [options]

[options] is shown in the website https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide

Use simple " for " loop to access subject files to batch extract brain of subjects

The whole codes are as bellows:

import subprocess
import os

nii_dir = '/home/linlin/Data/Images/MCI'  # root path
count = 0
for path, dirs, filepaths in os.walk(nii_dir)[:1]:  
   for filepath in filepaths[:1]:
       in_path_tmp = os.path.join(path, filepath)
       out_path_tmp = in_path_tmp[:len(in_path_tmp)-4] + '_bet.nii'
       # print ("input_path is {}noutput_path is {}nn".format(in_path_tmp, out_path_tmp))
       subprocess.call(['bet', in_path_tmp, out_path_tmp])
       count = count + 1
       print("count {}".format(count))