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/' +