package

JSON object

This object contains information about the squirrel package.

JSON variables

🔵 Primary key 🔴 Required

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

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

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

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

• 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

/