Brainstorm's Database Structure

Authors: Martin Cousineau, Raymundo Cassani

Understanding how data is organized and managed in Brainstorm is paramount for scripting your own pipelines, and adding new processes in the software. This page describes the structure of the Brainstorm database, and the metadata that is necessary to manage it.

On the hard drive

Brainstorm database resides on the hard drive at the database directory (brainstorm_db/). The database consists in an organized collection of protocols, where each protocol each with its own directory, which has a strict hierarchy, explained in the bullet list below:

TODO_RC: This information as tree image

• anat: This is where Anatomy files (e.g. MRI, surfaces) and subject's metadata are stored.

  • One folder per subject

    • brainstormsubject.mat: Metadata of the subject, see db_template('subjectmat')

    • subjectimage_*.mat: MRI files, see db_template('mrimat')

    • tess_*.mat: Surface files, see db_template('surfacemat')

• data: This is where Functional files (e.g. channels, recordings) and study's metadata are stored.

  • protocol.mat: All metadata of this protocol, as Matlab structs. See next section for details. Refer to variable ProtocolMat of function db_save().

  • protocol.db: All metadata of this protocol, as an SQLite database. See next section for details. Refer to sql_generate_db().

  • One folder per subject

    • One folder per study

      • brainstormstudy.mat: Metadata of the study, see db_template('studymat')

      • channel_*.mat: Channel files, see db_template('channelmat')

      • data_*.mat: Data (recording) files, see db_template('datamat')

      • Etc.

The files protocol.mat and protocol.db contain all the metadata that is required to manage the protocol data. In case any of this files is accidentaly deelted, or gets corrupted, protocol metadata can ge regenerated from (brainstormsubject.mat and brainstormstudy.mat).

All required metadata should always be saved on the hard drive outside of the protocol.mat / protocol.db files, such that if they get corrupted, deleted or one does a fresh reload of the database, there is no loss of information. This is why things like: which cortex file is selected, or which trials are marked as bad are also saved in separate files (brainstormsubject.mat and brainstormstudy.mat).

The filename of each file should always clearly indicate the basic type of the file, hence the required prefixes (e.g. data_*.mat).

The content of the structure of each .mat files is defined in db_template(), with the 'mat' suffix to differenciate from the in-memory metadata structure and the in-momery data structure of each type. For example:

• db_template('surfacemat'): Structure saved on the hard drive as a surface_*.mat file.

• db_template('loadedsurface'): Structure saved in memory containing all the data of a loaded surface_*.mat file.

• db_template('surface'): Structure saved in memory containing all the metadata of a surface_*.mat file, loaded from the protocol.db / protocol.mat file rather than the surface_*.mat file itself.

Protocol metadata

A brief paragraph describing why there are two versions, the main differences, and when is the user expected to see one or the other.

Matlab structure: protocol.mat

Once a protocol is loaded, Brainstorm has Matlab structures in memory that contain the metadata of all the files in this protocol. These are located in the GlobalData.DataBase global variable, such that it is easily accessible in any function of the software. It is defined db_template('GlobalData'). Let's walk through some of the important variables in this structure:

• GlobalData.DataBase.ProtocolInfo: Basic information about the protocols in the Brainstorm database folder, refer to db_template('ProtocolInfo').

  • Comment: Name of the protocol

  • STUDIES: Absolute path to the folder containing the functional data (/data/).

  • SUBJECTS: Absolute path to the folder containing the anatomical data (/anat/).

  • iStudy: Currently selected study, if applicable.

  • UseDefaultAnat: Protocol setting, whether new subjects should use the default anatomy by default.

  • UseDefaultChannel: Protocol setting, whether new subjects should share channel files by default.

• GlobalData.DataBase.ProtocolSubjects: Metadata of all subjects and their anatomical files of each loaded protocol, refer to db_template('ProtocolSubjects').

  • Subject: Metadata of all regular subjects, refer to db_template('subject').

  • DefaultSubject: Special subject used to store default anatomy. Same structure as regular subjects.

• GlobalData.DataBase.ProtocolStudies: Metadata of all studies and their functional files of each loaded protocol, refer to db_template('ProtocolStudies').

  • Study: Metadata of all regular studies, refer to db_template('study').

  • DefaultStudy: Special study used to store Common files, e.g. a global channel file. Same structure as regular studies.

  • AnalysisStudy: Special study to store Inter-subject files, e.g. stats results. Same structure as regular studies.

• GlobalData.DataBase.isProtocolLoaded: List of bool, whether the metadata of the protocol is already in memory or not. This is useful when you're running Brainstorm from the command line.

• GlobalData.DataBase.isProtocolModified: List of bool, whether the metadata of the protocol was modified and therefore the protocol.mat needs to be overwritten when Brainstorm closes.

• GlobalData.DataBase.iProtocol: The index of the currently selected protocol.

• GlobalData.DataBase.BrainstormDbDir: Absolute path to the brainstorm database directory.

• GlobalData.DataBase.DbVersion: Version number of the currently loaded protocol. Used to update the protocol structure when new fields are added to a specific file for example. Refer to db_update().

• GlobalData.DataBase.isReadOnly: Flag whether the user has write access to the protocol database directory. Used in tree_callbacks() to remove GUI option menus that would modify files.

• GlobalData.DataBase.LastSavedTime: Timestamp of the last time the protocol.mat file was overwritten. There used to be an automatic save when it had been a few hours.

• GlobalData.DataBase.Searches: Information about the search tabs of the database:

  • iActive: Index of the currently selected active search tab (0 if none).

  • Active: List of all active search tabs, with the first one being the whole database.

    • Name: Name of the tab, or empty if whole database

    • SearchNode: Tree structure representing the search query

    • AnatRootNode/FuncRootNode: The root node of the database tree, to avoid rebuilding the Java tree when you switch between tabs.

    • AnatSelNode/FuncSelNode: The currently selected node, to remember the last selected object before you switched between tabs.

  • All: If searches were saved between Brainstorm sessions, they are stored here.

    • Name: Name of the search

    • Search: Tree structure representing the search query

TODO: db_template('Subject'), db_template('Study'), db_template('Data'). etc

SQLite structure: protocol.db

TODO.