Configuration¶

Key configs: - configs/demo_config.json: small, fast defaults for demos. - configs/braingraph_default_config.json: fuller defaults for real runs. - configs/dsi_studio_config_schema.json: validation schema for extraction configs.

Important fields: - dsi_studio_cmd: absolute path to DSI Studio executable. - atlases, connectivity_values: keep fixed between Bayes and cross-validation to avoid metric-induced differences. - tract_count, tracking_parameters: parameters Bayes and cross-validation tune. - connectivity_options.connectivity_threshold: tuned in Bayes; propagated into apply/cross-val when seeded.

Validation: - scripts/run_pipeline.py, scripts/opticonn_hub.py, and the demos call JSON validation before running. - If DSI Studio is missing, errors include the download link.