bids_utils

BIDS dataset utilities using pybids.

Source: src/python/core/bids_utils.py

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Functions

summarize_bids_dataset

Summarize the contents of a BIDS dataset using pybids.

If bids_dir is not provided, loads it from the configuration file.

summarize_bids_dataset(bids_dir: Optional[str | Path] = None, config: Optional[Dict[str, Any]] = None, verbose: bool = True) -> Dict[str, Any]

Parameters

• bids_dir (str or Path, optional) — Path to the BIDS dataset directory. If None, loads from config.
• config (dict, optional) — Pre-loaded configuration dictionary. If None, loads from config files.
• verbose (bool, default=True) — If True, prints summary information to stdout.

Returns

dict Dictionary containing dataset summary with keys: - ‘dataset_path’: Path to the dataset - ‘n_subjects’: Number of subjects - ‘subjects’: List of subject IDs - ‘n_sessions’: Number of sessions (total across all subjects) - ‘sessions’: List of unique session IDs - ‘datatypes’: List of datatypes (e.g., ‘anat’, ‘func’) - ‘modalities’: List of modalities (e.g., ‘T1w’, ‘bold’) - ‘tasks’: List of task names (for func data) - ‘layout’: BIDSLayout object for further querying

Examples

>>> # Use config file
>>> summary = summarize_bids_dataset()
>>> print(f"Found {summary['n_subjects']} subjects")

>>> # Specify dataset path directly
>>> summary = summarize_bids_dataset('/path/to/bids/dataset')
>>> layout = summary['layout']
>>> files = layout.get(subject='01', suffix='T1w')

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get_subject_summary

Get a detailed summary of all files for a specific subject.

get_subject_summary(subject_id: str, layout: Optional[BIDSLayout] = None, bids_dir: Optional[str | Path] = None) -> pd.DataFrame

Parameters

• subject_id (str) — Subject ID (without ‘sub-‘ prefix)
• layout (BIDSLayout, optional) — Pre-initialized BIDSLayout object. If None, creates one from bids_dir.
• bids_dir (str or Path, optional) — Path to BIDS dataset. Required if layout is None.

Returns

pd.DataFrame DataFrame with one row per file, containing BIDS entities and file paths.

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