The squirrel format

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.

Background

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.

Installation

Pre-built packages are provided for common Linux distributions. Download the package matching your distribution, then install it with your package manager.

Releases are available here https://github.com/gbook/squirrel/releases

RHEL / AlmaLinux / Rocky (RHEL 8, 9, 10)

Install the .rpm matching your major release (el8, el9, or el10):

# RHEL 8
sudo dnf install ./squirrel-2026.8.482-1.el8.x86_64.rpm

# RHEL 9
sudo dnf install ./squirrel-2026.8.482-1.el9.x86_64.rpm

# RHEL 10
sudo dnf install ./squirrel-2026.8.482-1.el10.x86_64.rpm

Dependencies (openssl, p7zip, p7zip-plugins) are resolved automatically. The p7zip packages are in the EPEL repository, so enable it first if needed:

sudo dnf install epel-release

Ubuntu / Debian

Install the .deb matching your distribution:

# Ubuntu 22
sudo apt install ./squirrel_2026.8.482_ubuntu22.deb

# Ubuntu 24
sudo apt install ./squirrel_2026.8.482_ubuntu24.deb

# Debian 12
sudo apt install ./squirrel_2026.8.482_debian12.deb

Once installed, verify with:

squirrel --version

Documentation

https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format

Man page and web documentation

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 man

This 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