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.

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

JSON file

data/subjectID/studyNum/seriesNum/params.json

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.

JSON array

Array of series.

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.

JSON array

Array of imaging studies/sessions.

JSON array

Array of observations.

JSON array

Array of interventions.

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