LogoLogo
  • 🐿️NeuroInformatics Database
    • HIPAA Compliance
  • Getting Started
    • Installation
      • Quick Install
      • How to change passwords
      • Optional software
      • MySQL/MariaDB tweaks
    • Upgrade
      • Quick Upgrade
      • Migrate Existing Installation
  • Using NiDB
    • User's Guide
      • Importing data
      • Managing data
      • Finding & exporting data
      • Managing projects
      • Pipelines & analysis
      • Calendar
    • Administration
      • Front end (user facing)
      • Back end
      • nidb command line
  • Specifications
    • Data Storage Hierarchy
    • DICOM Anonymization
  • Tutorials
    • Working with Imaging Data
      • Uploading data for a sample project
      • Troubleshooting Missing Imaging Data
      • Import DICOM data
      • MR scan quality control
    • Manipulating Subjects, Studies, & Series
      • Working with subject IDs
      • Renaming series
    • Pipelines
    • Working with Redcap
      • Importing Data from a Redcap Project
      • Importing Subjects from Redcap
      • Reports based on data imported from Redcap
    • Analysis Builder
    • Administration of Users, Projects, & System
      • User Permissions
      • Creating new projects
      • Adding Users to Projects
      • Editing the config file
      • Deleting all the data
  • Contribute
    • Squirrel data sharing format
      • squirrel utilities
      • Using the squirrel library
      • Example package
      • squirrel vs BIDS
      • Specification v1.0
        • Package root
        • package
        • data
          • subjects
            • studies
              • series
                • params
              • analysis
            • observations
            • interventions
          • group-analysis
        • pipelines
          • data-steps
          • Pipeline scripts
        • experiments
        • data-dictionary
        • Modalities
      • Building squirrel library and utils
        • Building Python Wrapper
    • Building NiDB
    • Creating a Development VM
  • Help!
    • Github Issues
    • Github Discussions
Powered by GitBook
On this page
  • JSON variables
  • Variable options
  • Directory structure

Was this helpful?

Export as PDF
  1. Contribute
  2. Squirrel data sharing format
  3. Specification v1.0

package

JSON object

PreviousPackage rootNextdata

Last updated 11 months ago

Was this helpful?

This object contains information about the squirrel package.

JSON variables

Variable
Type
Default
Description

Changes

string

Any CHANGE files.

DataFormat

string

orig

Data format for imaging data to be written. Squirrel should attempt to convert to the specified format if possible. orig, anon, anonfull, nifti3d, nifti3dgz, nifti4d, nifti4dgz (see details below).

Datetime

datetime

Datetime the package was created.

Description

string

Longer description of the package.

License

string

Any sharing or license notes, or LICENSE files.

NiDBVersion

string

The NiDB version which wrote the package.

Notes

JSON object

See details below.

PackageName

string

Short name of the package.

PackageFormat

string

squirrel

Always squirrel.

Readme

string

Any README files.

SeriesDirectoryFormat

string

orig

orig, seq (see details below).

SquirrelVersion

string

Squirrel format version.

SquirrelBuild

string

Build version of the squirrel library and utilities.

StudyDirectoryFormat

string

orig

orig, seq (see details below).

SubjectDirectoryFormat

string

orig

orig, seq (see details below).

Variable options

subjectDirFormat, studyDirFormat, seriesDirFormat

  • orig - Original subject, study, series directory structure format. Example S1234ABC/1/1

  • seq - Sequential. Zero-padded sequential numbers. Example 00001/0001/00001

dataFormat

  • nifti3d - Nifti 3D format

    • Example file001.nii, file002.nii, file003.nii

  • nifti3dgz - gzipped Nifti 3D format

    • Example file001.nii.gz, file002.nii.gz, file003.nii.gz

  • nifti4d - Nifti 4D format

    • Example file.nii

  • nifti4dgz - gzipped Nifti 4D format

    • Example file.nii.gz

Notes

Notes about the package are stored here. This includes import and export logs, and notes from imported files. This is generally a freeform object, but notes can be divided into sections.

Section
Description

import

Any notes related to import. BIDS files such as README and CHANGES are stored here.

merge

Any notes related to the merging of datasets. Such as information about renumbering of subject IDs

export

Any notes related to the export process

Directory structure

Files associated with this section are stored in the following directory

/

Primary key Required

orig - Original, raw data format. If the original format was DICOM, the output format should be DICOM. See for details.

anon - If original format is DICOM, write anonymized DICOM, removing most PHI, except dates. See for details.

anonfull - If original format is DICOM, the files will be fully anonymized, by removing dates, times, locations in addition to PHI. See for details.

🔵
🔴
DICOM anonymization levels
DICOM anonymization levels
DICOM anonymization levels
🔴
🔴
🔵