squirrel is a neuroimaging data format to share every step of a neuroimaging analysis: experimental methods, raw data, analysis pipelines, and analyzed results. Multiple subjects, multiple sessions, multiple timepoints, clinical trial details, imaging and non-imaging data. If a user so desired, the squirrel format could be used to store the results of an entire R01 project from beginning to end in a single human-readable file. There is no miniumum amount of data needed to create a squirrel file: for example you can create a squirrel file with only an analysis pipeline and no data.
The squirrel neuroimaging data sharing format was developed as part of the open-source Neuroinformatics Database. The squirrel format specification is also open-source and freely available to include in open-source and commercial projects.
https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format
The CLI reference is maintained in doc/squirrel/squirrel.md. This file is the single source of truth for both the man page and the web documentation page.
When CLI options change, update squirrel.md and regenerate the man page:
make -C doc/squirrel manThis requires pandoc. Commit both squirrel.md and the regenerated squirrel.1 so the man page can be installed without pandoc as a dependency.
To preview the rendered man page locally:
make -C doc/squirrel view