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
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
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
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
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
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
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
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
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.
DataStepCount
number
🟡
Number of data steps.
VirtualPath
string
🟡
Path of this pipeline within the squirrel package.
series
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
studies
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.
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.
subjects
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.
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.
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