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)
