lesion_mask = os.path.join(data_dir, subject_id + '_' + X,
'lesion/lesion_mask_mni.nii.gz')
# define working dir
work_dir = os.path.join(out_dir, subject_id)
if not os.path.exists(work_dir):
os.makedirs(work_dir)
# go into working dir
os.chdir(work_dir)
lesion_mask_dil = os.path.join(work_dir, 'lesion_mask_mni_dilated.nii.gz')
print lesion_mask_dil
###### Step 1: dilating lesion mask #############################
dilate = DilateImage()
dilate.inputs.in_file = lesion_mask
dilate.inputs.operation = 'modal'
dilate.inputs.out_file = lesion_mask_dil
#print dilate.cmdline
dilate.run()
##### Step 2: get intra-subject gm mask #########################
rest_list = []
rest_str = []
i = 0
print "intra-subject rest mask ..."
for name in glob.glob(data_dir + subject_id + '*' +
'/preprocessed/func/connectivity/' +
