# squirrel-docs

## squirrel

- [Squirrel data sharing format](https://docs.neuroinfodb.org/squirrel/squirrel-data-sharing-format.md)
- [squirrel utilities](https://docs.neuroinfodb.org/squirrel/getting-started/squirrel-utilities.md): The squirrel command line program
- [info](https://docs.neuroinfodb.org/squirrel/getting-started/squirrel-utilities/info.md): How to use the squirrel info tool
- [extract](https://docs.neuroinfodb.org/squirrel/getting-started/squirrel-utilities/extract.md): Extract a copy of objects from the package
- [modify](https://docs.neuroinfodb.org/squirrel/getting-started/squirrel-utilities/modify.md): Modify the contents of a squirrel package
- [bids2squirrel](https://docs.neuroinfodb.org/squirrel/getting-started/squirrel-utilities/bids2squirrel.md): Convert BIDS format to squirrel format
- [dicom2squirrel](https://docs.neuroinfodb.org/squirrel/getting-started/squirrel-utilities/dicom2squirrel.md): Convert DICOM file(s) to squirrel format
- [Example package](https://docs.neuroinfodb.org/squirrel/getting-started/example-package.md)
- [Using the squirrel library](https://docs.neuroinfodb.org/squirrel/getting-started/using-the-squirrel-library.md): Overview of how to use the squirrel C++ library
- [Specification v1.0](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0.md): Format specification for v1.0
- [Package root](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/package-root.md): JSON object
- [package](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/package.md): JSON object
- [data](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data.md): JSON object
- [subjects](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects.md): JSON array
- [studies](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects/studies.md): JSON array
- [series](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects/studies/series.md): JSON array
- [params](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects/studies/series/params.md): Separate JSON file - params.json
- [analysis](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects/studies/analysis.md): JSON array
- [observations](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects/observations.md): JSON array
- [interventions](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/subjects/interventions.md): JSON array
- [group-analysis](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data/group-analysis.md): JSON array
- [pipelines](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/pipelines.md): JSON array
- [data-steps](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/pipelines/data-steps.md): JSON array
- [Pipeline scripts](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/pipelines/pipeline-scripts.md): Details about how pipeline scripts are formatted for squirrel and NiDB
- [experiments](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/experiments.md): JSON array
- [data-dictionary](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/data-dictionary.md): JSON object
- [Modalities](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/modalities.md)
- [JSON full listing](https://docs.neuroinfodb.org/squirrel/specifications/specification-v1.0/json-full-listing.md): Full listing of JSON fields in alphbetical order
- [squirrel vs BIDS](https://docs.neuroinfodb.org/squirrel/specifications/squirrel-vs-bids.md): Understanding the differences between package formats
- [DICOM Anonymization](https://docs.neuroinfodb.org/squirrel/specifications/dicom-anonymization.md): DICOM Anonymization Levels
- [Building squirrel library and utils](https://docs.neuroinfodb.org/squirrel/contribute/building-squirrel-library-and-utils.md)
- [Creating a Development VM](https://docs.neuroinfodb.org/squirrel/contribute/creating-a-development-vm.md): This describes how to create a Linux virtual machine to build NiDB


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