def extract_frommask_component(realigned_file, mask_file): import os import nibabel as nb import numpy as np from utils import mean_roi_signal from nipype import logging iflogger = logging.getLogger('interface') data = nb.load(realigned_file).get_data().astype('float64') mask = nb.load(mask_file).get_data().astype('float64') iflogger.info('Data and mask loaded.') mask_comp = mean_roi_signal(data, mask.astype('bool')) components_file = os.path.join(os.getcwd(), 'mask_mean_component.txt') iflogger.info('Saving components file:' + components_file) np.savetxt(components_file, mask_comp) return components_file
def extract_global_component(realigned_file): import os import nibabel as nb import numpy as np from utils import mean_roi_signal data = nb.load(realigned_file).get_data().astype('float64') mask = (data != 0).sum(-1) != 0 # Global Mask print 'Data loaded.' # Y = data[mask].T # Yc = Y - np.tile(Y.mean(0), (Y.shape[0], 1)) glb_comp = mean_roi_signal(data, mask) components_file = os.path.join(os.getcwd(), 'global_component.txt') print 'Saving components file:', components_file np.savetxt(components_file, glb_comp) return components_file