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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
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 .
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
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 (and possible values) |
|---|---|---|---|
| Variable | Description | Example |
|---|---|---|
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 |
|---|
{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.
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, white
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.
| number | Subject’s age in years at the time of the study. |
| datetime | Date of the study. |
| number | For repeated studies and clinical trials, this indicates the day number of this study in relation to time 0. |
| string | Study description. |
| string | Equipment name, on which the imaging session was collected. |
| number | Height in m of the subject at the time of the study. |
| string |
| number | Study number. May be sequential or correspond to NiDB assigned study number. |
| string | DICOM field |
| number | Similar to day number, but this should be an ordinal number. |
| string | Type of visit. ex: Pre, Post. |
| number | Weight in kg of the subject at the time of the study. |
| number | Number of analyses for this study. |
| number | Number of series for this study. |
| string | Relative path to the data within the package. |
JSON array | Array of series. |
JSON array | Array of analyses. |
| string |
| string | BIDS suffix |
| string | BIDS Task name |
| number | BIDS run number |
| string | BIDS PE direction |
| 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 |
|
JSON array
Interventions represent any substances or procedures administered to a participant; through a clinical trial or the participant’s use of prescription or recreational drugs. Detailed variables are available to record exactly how much and when a drug is administered. This allows searching by dose amount, or other variable.
The following examples convert between common language and the squirrel storage format
esomeprazole 20mg capsule by mouth daily
2 puffs atrovent inhaler every 6 hours
Defines the type of data. See table of supported .
entity (anat, fmri, dwi, etc)
Experiment name associated with this series. Experiments link to the section of the squirrel package
Primary key Required
| Variable | Type | Default | Description |
|---|
| Variable | Value |
|---|
| Variable | Value |
|---|
Primary key Required
| Variable | Type | Default | Description |
|---|
DrugClass | PPI |
DrugName | esomeprazole |
DoseAmount | 20mg |
DoseFrequency | daily |
Route | oral |
DoseUnit | mg |
DrugName | ipratropium |
DrugClass | bronchodilator |
DoseAmount | 2 |
DoseFrequency | every 6 hours |
AdministrationRoute | inhaled |
DoseUnit | puffs |
| string | Drug entry route (oral, IV, unknown, etc). |
| string | Date the record was created in the current database. The original record may have been imported from another database. |
| string | Date the record was first entered into a database. |
| string | Date the record was modified in the current database. |
| datetime | Datetime the intervention was stopped. |
| datetime | Datetime the intervention was started. |
| string | Longer description. |
| string | Full dosing string. Examples |
| number | In combination with other dose variables, the quantity of the drug. |
| string | Description of the frequency of administration. |
| string | For clinical trials, the dose key. |
| string | mg, g, ml, tablets, capsules, etc. |
| string | Drug class. |
| string | Name of the intervention. |
| string | Notes about drug. |
| string | Rater/experimenter name. |
| datetime | End datetime of the observation. |
| datetime | Date the record was created in the current database. The original record may have been imported from another database. |
| datetime | Date the record was first entered into a database. |
| datetime | Date the record was modified in the current database. |
| datetime | Start datetime of the observation. |
| string | Longer description of the measure. |
| number | Duration of the measure in seconds, if known. |
| string | Name of the instrument associated with this measure. |
| string | Name of the observation. |
| string | Detailed notes. |
| string | Name of the rater. |
| string | Value (string or number). |