import pandas as pd data_dir = os.environ.get('DATA_DIR') or '/home/daniel/fsl-analysis/data' study_name = os.environ.get('STUDY_NAME') or 'AV' raw_dir = os.path.join(data_dir, 'raw') behav_dir = os.path.join(data_dir, 'behavioral') op = OpenFMRIData(data_dir, raw_dir, study_name) # subject_names = ['HiAn'] # Specific subject names subject_names = op.get_subject_names() # All subjects for name in subject_names: subject_dir = op.create_subject_dir(name, overwrite=True) # if we want to create new data for analysis # subject_dir = op.create_subject_dir(name) # if we want to load new data for analysis # subject_dir = op.load_subject_dir(subname=name) create_events(subject_dir, behav_dir) analyzer = OpenFMRIAnalyzer(op,[subject_dir]) brain_image = analyzer.extract_brain(subject_dir) analyzer.estimate_bias_field(subject_dir, brain_image, overwrite=True) analyzer.anatomical_registration(subject_dir) analyzer.anatomical_smoothing(subject_dir) analyzer.slice_time_correction(subject_dir) analyzer.motion_correction(subject_dir) analyzer.functional_registration(subject_dir) analyzer.functional_smoothing(subject_dir)