JSON array
An array of imaging studies, with information about each study. An imaging study (or imaging session) is defined as a set of related series collected on a piece of equipment during a time period. An example is a research participant receiving an MRI exam. The participant goes into the scanner, has several MR images collected, and comes out. The time spent in the scanner and all of the data collected from it is considered to be a study.
Valid squirrel modalities are derived from the DICOM standard and from NiDB modalities. Modality can be any string, but some squirrel readers may not correctly interpret the modality or may convert it to “other” or “unknown”. See full list of modalities.
Files associated with this section are stored in the following directory. SubjectID and StudyNum are the actual subject ID and study number, for example /data/S1234ABC/1.
/data/<SubjectID>/<StudyNum>
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.
All DICOM tags are acceptable parameters. See this list for available DICOM tags https://exiftool.org/TagNames/DICOM.html. 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.
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
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 |
|---|---|---|---|
| Variable | Description | Example |
|---|---|---|
{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.
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 m of the subject at the time of the study.
Modality
string
Defines the type of data. See table of supported modalities.
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 kg 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.
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