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RF: Set FreeSurfer SUBJECTS DIR to default freesurfer
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nibabies/cli/parser.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -759,9 +759,9 @@ def parse_args(args=None, namespace=None):
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if config.execution.fs_subjects_dir is None:
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if output_layout == "bids":
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config.execution.fs_subjects_dir = output_dir / "sourcedata" / "infant-freesurfer"
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config.execution.fs_subjects_dir = output_dir / "sourcedata" / "freesurfer"
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elif output_layout == "legacy":
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config.execution.fs_subjects_dir = output_dir / "infant-freesurfer"
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config.execution.fs_subjects_dir = output_dir / "freesurfer"
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if config.execution.nibabies_dir is None:
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if output_layout == "bids":
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config.execution.nibabies_dir = output_dir

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