package

JSON object

This object contains information about the squirrel package.

JSON variables

*required

Variable	Type	Description
PackageFormat	string	Always squirrel.
SquirrelVersion	string	Squirrel format version.
SquirrelBuild	string	Build version of the squirrel library and utilities.
NiDBVersion	string	The NiDB version which wrote the package.
PackageName	string	Short name of the package.
Description	string	Longer description of the package.
Datetime	datetime	Datetime the package was created.
SubjectDirectoryFormat	string	orig, seq (see details below).
StudyDirectoryFormat	string	orig, seq (see details below).
SeriesDirectoryFormat	string	orig, seq (see details below).
DataFormat	string	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).
License	string	Any sharing or license notes, or LICENSE files.
Readme	string	Any README files.
Changes	string	Any CHANGE files.
Notes	JSON object	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

/