|
Size: 5233
Comment:
|
← Revision 61 as of 2022-08-22 14:14:32 ⇥
Size: 0
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Brainstorm architecture = == Brainstorm folders == Some more explanations about files and folders.<<BR>>Brainstorm needs '''different directories''', please try not to put everything at the same place, it won't work: * '''Program directory: '''"brainstorm3" * Contains all the program files: Matlab scripts, Java archives, documentation... * No user data in this folder: you can delete it and replace it with a new version, your data will be safe * Recommended location: * __Windows__: C:\Program Files\brainstorm3 * __Linux__: /home/username/brainstorm3 * __MacOS__: Documents/brainstorm3 * '''Database directory''': "brainstorm_db" * Created by user. * Contains all the Brainstorm database files. * Managed automatically by the application: do not move, delete or add files by yourself. * Recommended location: * __Windows__: C:\Program Files\brainstorm_db * __Linux__: /home/username/brainstorm_db * __MacOS__: Documents/brainstorm_db * '''User directory: '''".brainstorm" * Created automatically at Brainstorm startup. * Contains the database structure and the temporary folders * Typical location: * __Windows__: C:\Documents and Settings\username\.brainstorm * __Linux__: /home/username/.brainstorm * Contains: * __brainstorm.mat__: Matlab matrix where the Brainstorm options and database structure are stored. * __tmp/__: temporary directory used by some of the Brainstorm functions. Cleaned each time Brainstorm is started * '''Original data files''': * Recordings and anatomies you acquired and you want to process with Brainstorm. * Put them wherever you want''' __but not in any of the previous folders__'''. == Brainstorm database (concept) == 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). * 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. == Brainstorm database (files) == * Brainstorm_db folder created and managed completely from the Brainstorm graphic user interface (GUI) * All the files in the database have to be imported through the GUI: (right-click > Import...) * Imported files are stored in Matlab format (.mat files) at the appropriate place in the database folder. * Do not try to copy files by yourself in the brainstorm_db folder, it won't work * Based on the files/directories architecture: * __Anatomy data__: brainstorm_db/protocol_name/'''anat'''/subject_name * __Functional data__: brainstorm_db/protocol_name/'''data'''/subject_name/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 in .brainstorm * So 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. * It may happen when some process crashes, or if you move or add some files by yourself in the database folder. * If this happens, you will have to reload the current protocol (right-click popup menu > ''Reload'') or the whole database (menu ''File > Reload database'') == To remember == * __Different folders__ for: the '''program '''(brainstorm3), the '''database '''(brainstorm_db), and your '''original files'''. * Never modify the contents of the database folder by yourself * Do not put the original recordings in any of the Brainstorm folders, import them properly with the graphic interface |
Differences between revisions 4 and 61 (spanning 57 versions)