JSON full listing

Full listing of JSON fields in alphbetical order

JSON variables

🔵 Primary key 🔴 Required 🟡 Computed (squirrel writer/reader should handle these variables)

analysis

Variable	Type	Default	Description
DateStart	date	🔴	Datetime of the start of the analysis.
DateEnd	date		Datetime of the end of the analysis.
DateClusterStart	date		Datetime the job began running on the cluster.
DateClusterEnd	date		Datetime the job finished running on the cluster.
Hostname	string		If run on a cluster, the hostname of the node on which the analysis run.
PipelineName	string	🔴 🔵	Name of the pipeline used to generate these results.
PipelineVersion	number	1	Version of the pipeline used.
RunTime	number	0	Elapsed wall time, in seconds, to run the analysis after setup.
SeriesCount	number	0	Number of series downloaded/used to perform analysis.
SetupTime	number	0	Elapsed wall time, in seconds, to copy data and set up analysis.
Status	string		Status, should always be ‘complete’.
StatusMessage	string		Last running status message.
Successful	bool		Analysis ran to completion without error and expected files were created.
Size	number	🟡	Size in bytes of the analysis.
VirtualPath	string	🟡	Relative path to the data within the package.

data-dictionary

Variable	Type	Default	Description
DataDictionaryName	string	🔴	Name of this data dictionary.
NumFiles	number	🟡	Number of files contained in the experiment.
Size	number	🟡	Size, in bytes, of the experiment files.
VirtualPath	string	🟡	Path to the data-dictionary within the squirrel package.
data-dictionary-item	JSON array		Array of data dictionary items. See next table.

data-dictionary-item

Variable	Type	Default	Description
VariableType	string	🔴	Type of variable.
VariableName	string	🔴 🔵	Name of the variable.
Description	string		Description of the variable.
KeyValueMapping	string		List of possible key/value mappings in the format key1=value1, key2=value2. Example 1=Female, 2=Male
ExpectedTimepoints	number		Number of expected timepoints. Example, the study is expected to have 5 records of a variable.
RangeLow	number		For numeric values, the lower limit.
RangeHigh	number		For numeric values, the upper limit.

group-analysis

Variable	Type	Default	Description
Datetime	datetime		Datetime of the group analysis.
Description	string		Description.
GroupAnalysisName	string	🔴 🔵	Name of this group analysis.
Notes	string		Notes about the group analysis.
FileCount	number	🟡	Number of files in the group analysis.
Size	number	🟡	Size in bytes of the analysis.
VirtualPath	string	🟡	Path to the group analysis data within the squirrel package.

experiments

Variable	Type	Default	Description
ExperimentName	string	🔴 🔵	Unique name of the experiment.
FileCount	number	🟡	Number of files contained in the experiment.
Size	number	🟡	Size, in bytes, of the experiment files.
VirtualPath	string	🟡	Path to the experiment within the squirrel package.

interventions

Variable	Type	Default	Description
AdministrationRoute	string		Drug entry route (oral, IV, unknown, etc).
DateRecordCreate	string		Date the record was created in the current database. The original record may have been imported from another database.
DateRecordEntry	string		Date the record was first entered into a database.
DateRecordModify	string		Date the record was modified in the current database.
DateEnd	datetime		Datetime the intervention was stopped.
DateStart	datetime	🔴	Datetime the intervention was started.
Description	string		Longer description.
DoseString	string	🔴	Full dosing string. Examples tylenol 325mg twice daily by mouth, or 5g marijuana inhaled by volcano
DoseAmount	number		In combination with other dose variables, the quantity of the drug.
DoseFrequency	string		Description of the frequency of administration.
DoseKey	string		For clinical trials, the dose key.
DoseUnit	string		mg, g, ml, tablets, capsules, etc.
InterventionClass	string		Drug class.
InterventionName	string	🔴 🔵	Name of the intervention.
Notes	string		Notes about drug.
Rater	string		Rater/experimenter name.

observations

Variable	Type	Default	Description
DateEnd	datetime		End datetime of the observation.
DateRecordCreate	datetime		Date the record was created in the current database. The original record may have been imported from another database.
DateRecordEntry	datetime		Date the record was first entered into a database.
DateRecordModify	datetime		Date the record was modified in the current database.
DateStart	datetime	🔴	Start datetime of the observation.
Description	string		Longer description of the measure.
Duration	number		Duration of the measure in seconds, if known.
InstrumentName	string		Name of the instrument associated with this measure.
ObservationName	string	🔴 🔵	Name of the observation.
Notes	string		Detailed notes.
Rater	string		Name of the rater.
Value	string	🔴	Value (string or number).

package

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).

pipelines

Variable	Type	Default	Description
ClusterType	string		Compute cluster engine (sge or slurm).
ClusterUser	string		Submit username.
ClusterQueue	string		Queue to submit jobs.
ClusterSubmitHost	string		Hostname to submit jobs.
CompleteFiles	JSON array		JSON array of complete files, with relative paths to analysisroot.
CreateDate	datetime	🔴	Date the pipeline was created.
DataCopyMethod	string		How the data is copied to the analysis directory: cp, softlink, hardlink.
DependencyDirectory	string
DependencyLevel	string
DependencyLinkType	string
Description	string		Longer pipeline description.
DirectoryStructure	string
Directory	string		Directory where the analyses for this pipeline will be stored. Leave blank to use the default location.
Group	string		ID or name of a group on which this pipeline will run
GroupType	string		Either subject or study
Level	number	🔴	subject-level analysis (1) or group-level analysis (2).
MaxWallTime	number		Maximum allowed clock (wall) time in minutes for the analysis to run.
ClusterMemory	number		Amount of memory in GB requested for a running job.
PipelineName	string	🔴 🔵	Pipeline name.
Notes	string		Extended notes about the pipeline
NumberConcurrentAnalyses	number	1	Number of analyses allowed to run at the same time. This number if managed by NiDB and is different than grid engine queue size.
ClusterNumberCores	number	1	Number of CPU cores requested for a running job.
ParentPipelines	string		Comma separated list of parent pipelines.
ResultScript	string		Executable script to be run at completion of the analysis to find and insert results back into NiDB.
SubmitDelay	number		Delay in hours, after the study datetime, to submit to the cluster. Allows time to upload behavioral data.
TempDirectory	string		The path to a temporary directory if it is used, on a compute node.
UseProfile	bool		true if using the profile option, false otherwise.
UseTempDirectory	bool		true if using a temporary directory, false otherwise.
Version	number	1	Version of the pipeline.
PrimaryScript	string	🔴	See details of pipeline scripts
SecondaryScript	string		See details of pipeline scripts.
DataStepCount	number	🟡	Number of data steps.
VirtualPath	string	🟡	Path of this pipeline within the squirrel package.
data-steps	JSON array		See data specifications

series

Variable	Type	Default	Description
BidsEntity	string		BIDS entity (anat, fmri, dwi, etc)
BidsSuffix	string		BIDS suffix
BIDSTask	string		BIDS Task name
BIDSRun	number		BIDS run number
BIDSPhaseEncodingDirection	string		BIDS PE direction
Description	string		Description of the series
ExperimentName	string		Experiment name associated with this series. Experiments link to the experiments section of the squirrel package
Protocol	string	🔴	Protocol name
Run	number		The run identifies order of acquisition in cases of multiple identical series.
SeriesDatetime	date	🔴	Date of the series, usually taken from the DICOM header
SeriesNumber	number	🔴 🔵	Series number. May be sequential, correspond to NiDB assigned series number, or taken from DICOM header
SeriesUID	string		From the SeriesUID DICOM tag
BehavioralFileCount	number	🟡	Total number of beh files (including files in subdirs)
BehavioralSize	number	🟡	Size of beh data, in bytes
FileCount	number	🟡	Total number of files (including files in subdirs)
Size	number	🟡	Size of the data, in bytes
params	JSON file		data/subjectID/studyNum/seriesNum/params.json
analysis	JSON object

studies

Variable	Type	Default	Description
AgeAtStudy	number	🔴	Subject’s age in years at the time of the study.
Datetime	datetime	🔴	Date of the study.
DayNumber	number		For repeated studies and clinical trials, this indicates the day number of this study in relation to time 0.
Description	string	🔴	Study description.
Equipment	string		Equipment name, on which the imaging session was collected.
Height	number		Height in meters of the subject at the time of the study.
Modality	string	🔴	Defines the type of data. See table of supported modalities.
Notes	string		Any notes about the study
StudyNumber	number	🔴 🔵	Study number. May be sequential or correspond to NiDB assigned study number.
StudyUID	string		DICOM field StudyUID.
TimePoint	number		Similar to day number, but this should be an ordinal number.
VisitType	string		Type of visit. ex: Pre, Post.
Weight	number		Weight in kilograms of the subject at the time of the study.
AnalysisCount	number	🟡	Number of analyses for this study.
SeriesCount	number	🟡	Number of series for this study.
VirtualPath	string	🟡	Relative path to the data within the package.
series	JSON array		Array of series.
analyses	JSON array		Array of analyses.

subjects

Variable	Type	Default	Description (and possible values)
AlternateIDs	JSON array		List of alternate IDs. Comma separated.
DateOfBirth	date	🔴	Subject’s date of birth. Used to calculate age-at-study. Value can be YYYY-00-00 to store year only, or YYYY-MM-00 to store year and month only.
Gender	char		Gender.
GUID	string		Globally unique identifier, from the NIMH Data Archive (NDA).
Ethnicity1	string		NIH defined ethnicity: Usually hispanic, non-hispanic
Ethnicity2	string		NIH defined race: americanindian, asian, black, hispanic, islander, white
Notes	string		Notes about this subject
Sex	char	🔴	Sex at birth (F,M,O,U).
SubjectID	string	🔴 🔵	Unique ID of this subject. Each subject ID must be unique within the package.
InterventionCount	number	🟡	Number of intervention objects.
ObservationCount	number	🟡	Number of observation objects.
StudyCount	number	🟡	Number of studies.
VirtualPath	string	🟡	Relative path to the data within the package.
studies	JSON array		Array of imaging studies/sessions.
observations	JSON array		Array of observations.
interventions	JSON array		Array of interventions.