Autonima

Autonima is a usage-first toolkit for automated neuroimaging review workflows: search PubMed, screen studies with LLMs, retrieve full text, parse coordinates, and generate outputs for downstream meta-analysis.

The documentation here is focused on how to run the CLI and how to author a working config.yml. It is intentionally not a full Python API reference.

Who This Is For

• Researchers running systematic-review style neuroimaging pipelines from the command line
• Users preparing reproducible config.yml files for search, screening, retrieval, parsing, and annotation
• Maintainers who need a stable reference for the CLI surface and the expected output layout

Workflow

1. Install autonima and any optional extras you need.
2. Generate a starting config with autonima create-sample-config.
3. Edit the config for your search query, screening criteria, and retrieval setup.
4. Validate it with autonima validate config.yaml.
5. Run the pipeline with autonima run config.yaml.
6. Optionally run autonima meta OUTPUT_FOLDER on the generated NiMADS outputs.

Start Here

• Installation
• Quickstart
• Configuration Guide
• CLI Usage Guide
• Outputs Guide
• Interpreting Outputs
• CLI Reference

Important Notes

• run and validate use positional arguments: autonima run CONFIG [OUTPUT_FOLDER].
• If you omit OUTPUT_FOLDER, the CLI defaults to a sibling directory derived from the config file stem. Example: projects/cue_reactivity/default.yaml becomes projects/cue_reactivity/default/.
• The config file still needs a non-empty output.directory field because configuration validation currently requires it.