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@@ -57,7 +57,6 @@ def read_hippocampal_volume_file_dataframe(volume_file_path: str) -> pandas.Data
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def main():
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- # TODO add description
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argparser = argparse.ArgumentParser(
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description='Read hippocampal volumes computed by Freesurfer'
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'\nhttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields')
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@@ -66,8 +65,10 @@ def main():
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help='default: %(default)s')
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argparser.add_argument('--output-format', choices=['csv'], default='csv',
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help='default: %(default)s')
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- # TODO default to $SUBJECTS_DIR
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- argparser.add_argument('root_dir_path')
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+ argparser.add_argument('root_dir_path',
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+ nargs='?' if 'SUBJECTS_DIR' in os.environ else 1,
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+ default=os.environ.get('SUBJECTS_DIR', None),
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+ help='default: $SUBJECTS_DIR (%(default)s)')
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args = argparser.parse_args()
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volume_file_paths = find_hippocampal_volume_files(
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root_dir_path=args.root_dir_path,
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