Examples

Example inputs and outputs from Neurobagel tools.

api-responses/

Examples of responses returned by Neurobagel APIs.

data-upload/

Examples of valid input files for Neurobagel harmonization tools, including resultant Neurobagel graph-ready dataset files.

• example_synthetic.tsv: valid phenotypic tabular data file (has participant and session IDs corresponding to the synthetic bids-examples dataset)
• example_synthetic_participants.json: valid BIDS data dictionary without Neurobagel annotations, ready to be used in the annotation tool along with example_synthetic.tsv
• example_synthetic.json: valid phenotypic data dictionary for example_synthetic.tsv containing Neurobagel annotations
• example_synthetic.jsonld: example graph-ready subject data file for a purely phenotypic dataset. Contains subject-level annotated phenotypic attributes. Obtained by applying the data dictionary (.json) to the original tabular data (.tsv) using the bagel pheno command.
• nipoppy_proc_status_synthetic.tsv: valid Nipoppy processing pipeline status file (has participant and session IDs drawn from a subset of bids-examples synthetic)

pheno-bids-output/

Example graph-ready data files containing harmonized phenotypic and raw imaging (meta)data.

• example_synthetic_pheno-bids.jsonld: Sample output of bagel bids command on example_synthetic.jsonld and the synthetic bids-examples dataset. Contains subject-level annotated imaging metadata (inferred from the BIDS directory structure) on top of the subject-level annotated phenotypic attributes.

pheno-derivatives-output/

Example graph-ready data files containing harmonized phenotypic and imaging derivative (meta)data.

• example_synthetic_pheno-derivatives.jsonld: Sample output of bagel derivatives command on example_synthetic.jsonld and nipoppy_proc_status_synthetic.tsv. Contains subject-level imaging derivative metadata on top of the subject-level annotated phenotypic attributes.

pheno-bids-derivatives-output/

Example graph-ready data files containing harmonized phenotypic, raw imaging, and imaging derivative (meta)data.

• example_synthetic_pheno-bids-derivatives.jsonld: Sample output when bagel pheno, bagel bids, and bagel derivatives commands have all been run, using example_synthetic.tsv, bids-examples synthetic, and nipoppy_proc_status_synthetic.tsv. Contains subject-level raw imaging and imaging derivative metadata on top of the subject-level annotated phenotypic attributes.

query-tool-results/

Example downloadable query result TSV files from the Neurobagel query tool.