# JSON full listing ### JSON variables :blue\_circle: Primary key\ :red\_circle: Required\ :yellow\_circle: 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

Variable	Type	Default	Description
`GroupAnalysisCount`	number	🟡	Number of group analyses.
`SubjectCount`	number	🟡	Number of subjects in the package.
subjects	JSON array		Array containing the subjects.
group-analysis	JSON array		Array containing group analyses.

## 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.
`VariableDescription`	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.

## data-steps

Variable	Type	Default	Description
`SearchAssociationType`	string	🔴	[Search] `study`, or `subject`.
`ExportBehavioralDirectoryName`	string		[Export] if `BehFormat` writes data to a sub directory, the directory should be named this.
`ExportBehavioralDirectoryFormat`	string		[Export] `nobeh`, `behroot`, `behseries`, `behseriesdir`
`ExportDataFormat`	string	🔴	[Export] `native`, `dicom`, `nifti3d`, `nifti4d`, `analyze3d`, `analyze4d`, `bids`.
`Enabled`	bool	🔴	[Search] `true` if the step is enabled, `false` otherwise
`ExportGzip`	bool		[Export] `true` if converted Nift data should be g-zipped, `false` otherwise.
`SearchImageType`	string		[Search] Comma separated list of image types, often derived from the DICOM ImageType tag, (0008:0008).
`DataLevel`	string	🔴	[Search] `nearestintime`, `samestudy`. Where is the data coming from.
`Location`	string		[Export] Directory, relative to the `analysisroot`, where this data item will be written.
`Modality`	string	🔴	[Search] Modality to search for.
`NumberBOLDreps`	string		[Search] If `SeriesCriteria` is set to `usecriteria`, then search based on this option.
`NumberImagesCriteria`	string		[Search]
`Optional`	bool	🔴	[Search] `true` if this data step is option. `false` if this step is required and the analysis will not run if the data step is not found.
`Order`	number	🔴	The numerical order of this data step.
`PreserveSeries`	bool		[Export] `true` to preserve series numbers or `false` to assign new ordinal numbers.
`PrimaryProtocol`	bool		[Search] `true` if this data step determines the primary study, from which subsequent analyses are run.
`Protocol`	string	🔴	[Search] Comma separated list of protocol name(s).
`SeriesCriteria`	string	🔴	[Search] Criteria for which series are downloaded if more than one matches criteria: `all`, `first`, `last`, `largest`, `smallest`, `usecriteria`.
`UsePhaseDirectory`	bool		[Export] `true` to write data to a sub directory based on the phase encoding direction.
`UseSeriesDirectory`	bool		[Export] `true` to write each series to its own directory, `false` to write data to the root export directory.

## 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).

## params

Variable	Description	Example
{Key:Value}	A unique key, sometimes derived from the DICOM header	Protocol, T1w FieldStrength, 3.0

## 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).
`EnrollmentGroup`	string		Enrollment group. Example: patient, control, etc.
`EnrollmentStatus`	string		Project enrollment status: excluded, completed, etc.
`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.

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