🐿️Squirrel data sharing format
Overview
The squirrel data sharing format is designed to allow easy sharing of neuroimaging data. All research imaging data can be categorized into one of 10 object types. Squirrel organizes these objects into a heirarchy, allowing sharing of complex datasets that span raw data (and experiments used to collect it) to analyzed data (and the methods used to analyze), and everything in between.
Get squirrel
Squirrel utilities are available from our github repository: https://github.com/gbook/squirrel/releases
Package installers are available for
RHEL 8 and compatible
RHEL 9 and compatible
RHEL 10 and compatible
debian 12
Ubuntu 24
Source code is avilable to build squirrel utilities or library.
Squirrel object types
All neuroimaging data can be categorized into one of these 10 object types
analysis
Analysis results
freesurfer analysis results
data-dictionary
Data dictionary with key-value pairs to describe variables
Female=1, Male=2...
experiment
An experiment used to collect raw data. Can include task instructions, or behavioral data analysis scripts
A go-no-go task; with ePrime files
group-analysis
Contains all data related to a group analysis
intervention
Data about something administered to the subject
Drug dosing information
observation
Data about something observed from the subject
PANS, SCID, etc
pipeline
Analysis pipeline script; with extra script or other files necessary to perform the analysis.
A script to run an FSL analysis
series
Unique imaging series. A study can have more than one imaging series.
T1w from an MRI
study
Unique imaging session. A subject can have more than one study
A set of MRI images collected during a scan session
subject
Unique subject
A human, monkey, bacteria, etc
Contribute
Squirrel format is open-source and we are always looking for contributions.
Publications
Book GA, Calhoun VD, Stevens MC, Pearlson GD. Sharing Neuroimaging Data with Squirrel - A Relational Data Format to Store Raw to Analyzed Data and Everything in Between. Neuroinformatics. 2025 Jul 3;23(3):37. doi: 10.1007/s12021-025-09732-7. PMID: 40610663.
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