Basic concepts

Brainstorm database

Brainstorm toolbox allows you to classify your recordings and analysis with three different levels of definition:

• Protocol

  • Some people would prefer to call this experiment or study.

  • It can designate all the data that were acquired on one or several subjects, with the same objectives (study of a specific cognitive task, epileptic spikes localization, functional differences between two populations).
  • Each protocol may include one or several subjects.
  • Default data can be defined at the protocol level. If you cannot get the individual MR images of all or some of your subjects, you can use a default anatomy. If you want to localize the sources for an EEG recording but do not know the location of each electrode in space, you can use standardized electrodes positions.

• Subject

  • A person who participated in a given protocol.
  • You need two categories of information to define a subject:
    • Files describing the subject's anatomy : MRI and surfaces
    • Functional data files, ie. files that have a temporal dimension or that are related to a precise recording session: EEG / MEG recordings, definition of the sensors, source estimations, statistical results...

• Condition

  • For each subject, functional files can be classified in different experimental conditions.

  • This level of definition is also used to separate different runs (ie. recording sessions) for the same subject.

Some Brainstorm database properties:

• It is created and managed completely from the Brainstorm GUI (tree in the main interface window)
• It is based on the files/directories architecture:

  • Anatomy data in: protocol_name/subject_name/anat/

  • Functional data in: protocol_name/subject_name/data/condition_name/

  • Each file you see in the Brainstorm window corresponds to a proper file on the hard drive; but the contrary is not necessarily true. There are extra information stored in each directory, to save properties, comments, default data, links between different items, etc.
  • For this reason, you should not try to manipulate directly the files in the Brainstorm database directory.
• Database structure in memory:

  • A copy of the database structure is saved by Brainstorm in your home directory (~username on Linux, Documents and settings\username on Windows),

  • so that when you start the program or change protocol, there is no need to read again all the files on the hard drive (this may take some time).
  • As a consequence, the files that are displayed in the Brainstorm window may differ from what is actually on the disk (if some process crashed, or if you moved or add some files by yourself)

  • If this happens, you will have to reload the current protocol (popup menu Reload) or the whole database (menu File > Reload database)

Default anatomy

For each protocol or subject, you can chose between using your own anatomy files, or the the ones that are provided with Brainstorm.

• The default anatomy is based on the Colin27 MRI volume provided by the Montreal Neurological Institute: an average of 27 T1-weighted scans of Colin Holmes brain.

• Many surfaces are provided with this default anatomy; they were extracted with different programs: BrainVisa, BrainSuite, and FreeSurfer.

• The default scalp comes from ?FreeSurfer, the default skull surfaces from ?BrainSuite, and the default cortical surface from ?BrainVisa.

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