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.

JSON variables

🔵 Primary key 🔴 Required 🟡 Computed (squirrel writer/reader should handle these variables)

Directory structure

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>

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.

JSON variables

🔵 Primary key 🔴 Required 🟡 Computed (squirrel writer/reader should handle these variables)

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 to store data collection parameters.

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.

Analysis results, run on an imaging study level. Can contain files, directories, and variables.

JSON variables

🔵 Primary key 🔴 Required 🟡 Computed (squirrel writer/reader should handle these variables)