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| = Tutorial 1: Brainstorm architecture = ''Authors: Francois Tadel, Sylvain Baillet'' <<BR>>You should read this page carefully, in order to understand how the program is organized. If you don't follow a few simple rules reminded at the bottom of the page, Brainstorm may not work properly. <<TableOfContents(2,2)>> == Brainstorm folders == Brainstorm needs '''different directories''', please try not to put everything at the same place. '''<<BR>>1. Program directory: '''"brainstorm3" * Contains all the program files: Matlab scripts, compiled binaries, templates, etc. * There is no user data in this folder. * You can delete it and replace it with a newer version at anytime, your data will be safe. * Recommended location: * '''Windows''': My documents\brainstorm3 * '''Linux''': /home/username/brainstorm3 * '''MacOS''': Documents/brainstorm3 <<BR>>'''2. 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''': My documents\brainstorm_db * '''Linux''': /home/username/brainstorm_db * '''MacOS''': Documents/brainstorm_db <<BR>>'''3. User directory: '''".brainstorm" * Created automatically at Brainstorm startup. Typical location:<<BR>> * '''Windows''': C:\Documents and Settings\username\.brainstorm * '''Linux''': /home/username/.brainstorm * '''MacOS''': /Users/username/.brainstorm * Contains: * '''brainstorm.mat''': Brainstorm user preferences. * '''tmp/''': Temporary folder, cleaned every time Brainstorm is started.<<BR>>You may have to change the location of the temporary folder if you have a limited amount of storage or a limited quota in your home folder. * '''process/''': Personal plugins folder. * '''reports/''': Process reports. * '''openmeeg/''': OpenMEEG binaries (downloaded automatically when needed) * '''templates/''': Additional anatomy templates, saved as .zip files. * '''mex/''': Some mex files that have to be recompiled. <<BR>>'''4. Original data files''': * Recordings you acquired and you want to process with Brainstorm. * Put them wherever you want''' __but not in any of the previous folders__'''. == Database structure == Brainstorm allows you to organize your recordings and analysis with three levels of definition: * '''Protocol''' * Group of datasets that have to be processed or displayed together. * A protocol can include one or several subjects. * Some people would prefer to call this ''experiment ''or ''study''. * You can only open one protocol at a time. * '''Subject''' * A person who participated in a given protocol. * A subject contains two categories of information: anatomy and functional data. * Anatomy: Includes at least an MRI volume and some surfaces extracted from the MRI. * Functional data: Everything that is related with the MEG/EEG acquisition. * For each subject, it is possible to use either the actual MRI of the person or one of the anatomy templates available in Brainstorm. * '''Sub-folders ''' * For each subject, the functional files can be organized in different sub-folders. * These folders can represent different recordings sessions (aka acquisition runs) or different experimental conditions. * The current structure of the database does not allow to have more that one level of sub-folders for each subject. It is not possible to organize the files by session AND by condition.<<BR>><<BR>> {{attachment:db.gif}} == Database files == * Brainstorm_db folder is 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/brainstorm.mat ''' * 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 with the graphic interface<<BR>> == Feedback == <<EmbedContent(http://neuroimage.usc.edu/brainstorm3_register/get_feedback.php?Tutorials/BstFolders)>> == Next == It is finally time to start Brainstorm. [[Tutorials/TutFirstSteps|Next tutorial]]. |
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