def brain_extraction(input_filename, output_filename=None):
print 'Brain extraction ...'
if output_filename == None:
filename_save = input_filename.split('.')[0]+'_bet.nii.gz'
else:
filename_save = os.path.abspath(output_filename)
bet(input_filename, filename_save,options=' -R -F -f .2 -g 0')
print "Saving to:", filename_save
return filename_save
if root.endswith('MPRAGE_1_from_structual_T1Space'):
# anatomy bet
base_dir = root+'/'
#filename = 'T1_anatomy.nii.gz'
filename = 'fbrain1_mprage1.nii.gz'
base_filename = base_dir + filename
#bet(base_filename, root+'/fbrain0_mprage1_bet.nii.gz',options=' -R -f .2 -g 0')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .4 -g -0.05 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .2 -g -0.02 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .1 -g -0.02 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .15 -g 0.0 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -R -f .2 -g 0.0 -c 151 177 90')
bet(base_filename, root+'/bet_new.nii.gz',options=' -R -f .2 -g 0.0 -c 151 177 90')
'''
if root.endswith('DTI'):
#difusion tensor image - brain extraction
base_dir = root+'/'
filename = 'raw.nii.gz'
base_filename = base_dir + filename
bet(base_filename, root+'/raw_bet.nii.gz',options=' -R -F -f .2 -g 0')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .4 -g -0.05 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .2 -g -0.02 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .1 -g -0.02 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -F -f .15 -g 0.0 -c 151 177 90')
#bet(base_filename, root+'/rawbet.nii.gz',options=' -R -f .2 -g 0.0 -c 151 177 90')
