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JSON array
An array of series. Basic series information is stored in the main squirrel.json file. Extended information including series parameters such as DICOM tags are stored in a params.json file in the series directory.
Files associated with this section are stored in the following directory. subjectID, studyNum, seriesNum are the actual subject ID, study number, and series number. For example /data/S1234ABC/1/1.
/data/<SubjectID>/<StudyNum>/<SeriesNum>
Behavioral data is stored in
/data/<SubjectID>/<StudyNum>/<SeriesNum>/beh
Separate JSON file - params.json
Series collection parameters are stored in a separate JSON file called params.json stored in the series directory. The JSON object is an array of key-value pairs. This can be used for MRI sequence parameters.
Files associated with this section are stored in the following directory. subjectID, studyNum, seriesNum are the actual subject ID, study number, and series number. For example /data/S1234ABC/1/1.
/data/<SubjectID>/<StudyNum>/<SeriesNum>/params.json
JSON array
This object is an array of group analyses. A group analysis is considered an analysis involving more than one subject.
Files associated with this section are stored in the following directory, where <GroupAnalysisName> is the name of the analysis.
/group-analysis/<GroupAnalysisName>/
Primary key Required Computed (squirrel writer/reader should handle these variables)
Primary key Required Computed (squirrel writer/reader should handle these variables)
| Variable | Type | Default | Description |
|---|---|---|---|
Primary key Required Computed (squirrel writer/reader should handle these variables)
| Variable | Type | Default | Description (and possible values) |
|---|---|---|---|
All DICOM tags are acceptable parameters. See this list for available DICOM tags . Variable keys can be either the hexadecimal format (ID) or string format (Name). For example 0018:1030 or ProtocolName. The params object contains any number of key/value pairs.
| Variable | Description | Example |
|---|
Primary key Required Computed (squirrel writer/reader should handle these variables)
| Variable | Type | Default | Description |
|---|
{Key:Value} | A unique key, sometimes derived from the DICOM header | Protocol, T1w FieldStrength, 3.0 |
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.
BidsEntity
string
BIDS entity (anat, fmri, dwi, etc)
BidsSuffix
string
BIDS suffix
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
AlternateIDs
JSON array
List of alternate IDs. Comma separated.
DateOfBirth
date
Subject’s date of birth. Used to calculate age-at-server. 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 NDA.
Ethnicity1
string
NIH defined ethnicity: Usually hispanic, non-hispanic
Ethnicity2
string
NIH defined race: americanindian, asian, black, hispanic, islander,