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>
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)
| Variable | Type | Default | Description |
|---|---|---|---|
| Variable | Description | Example |
|---|---|---|
{Key:Value}
A unique key, sometimes derived from the DICOM header
Protocol, T1w FieldStrength, 3.0
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.
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
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 |
|---|
Variable | Type | Default | Description |
| date | Datetime of the start of the analysis. |
| date | Datetime of the end of the analysis. |
| date | Datetime the job began running on the cluster. |
| date | Datetime the job finished running on the cluster. |
| string | If run on a cluster, the hostname of the node on which the analysis run. |
| string | Name of the pipeline used to generate these results. |
| number |
| Version of the pipeline used. |
| number |
| Elapsed wall time, in seconds, to run the analysis after setup. |
| number |
| Number of series downloaded/used to perform analysis. |
| number |
| Elapsed wall time, in seconds, to copy data and set up analysis. |
| string | Status, should always be ‘complete’. |
| string | Last running status message. |
| bool | Analysis ran to completion without error and expected files were created. |
| number | Size in bytes of the analysis. |
| string | Relative path to the data within the package. |
| string |
| string | BIDS suffix |
| string | Description of the series |
| string |
| string | Protocol name |
| number | The run identifies order of acquisition in cases of multiple identical series. |
| date | Date of the series, usually taken from the DICOM header |
| number | Series number. May be sequential, correspond to NiDB assigned series number, or taken from DICOM header |
| string | From the SeriesUID DICOM tag |
| number | Total number of beh files (including files in subdirs) |
| number | Size of beh data, in bytes |
| number | Total number of files (including files in subdirs) |
| number | Size of the data, in bytes |
JSON file |
|
JSON object |
|
entity (anat, fmri, dwi, etc)
Experiment name associated with this series. Experiments link to the section of the squirrel package