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| = Tutorial 1: Brainstorm architecture = 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 will not work properly. <<TableOfContents(2,2)>> == Brainstorm folders == Brainstorm needs '''different directories''', please try not to put everything at the same place: * '''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''': My documents\brainstorm3 * '''Linux''': /home/username/brainstorm3 * '''MacOS''': Applications/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''': My documents\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<<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/''': this is where you should add your custom processes files (will be reminded later) * '''reports/''': where the process reports are saved * '''openmeeg/''': OpenMEEG binaries will be downloaded automatically to this folder if you compute any BEM headmodel * '''templates/''': Your own personal template anatomies, saved as .zip files. They can be downloaded from the website and you can create new ones * '''mex/''': some mex files that have to be recompiled, in case you don't have the write access in the Brainstorm folder * '''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 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. * For example, when adding a new subject, the "Default channel file" option asks you if you have many ("no" option) or only one ("yes" option) recording sessions (''i.e. ''condition) per subject. == Brainstorm 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'') == Brainstorm processing steps == For each subject Brainstorm needs to go through the following processing steps: * ''Import MRI'' (or surfaces etc), or use the ''Default anatomy'' * ''Review raw file'': continuous data files are read and the pre-processing steps are performed. Standard processing steps include (but are not restricted to): co-registration with MRI; power-line noise removal; DC offset removal (''i.e.'' high-pass filtering); estimation of blink and cardiac artifacts; estimation of bad channels or data segments; sorting of the triggers (events) of interest etc. * ''Import MEG/EEG: '''''Only after''' having reviewed the raw files (and applied many pre-processing steps) the data are fully imported in Brainstorm. This is the step where they are organized in '''epoch segments''' (via the triggers). * ''Advanced processing:'' Then, source-reconstruction, time-frequency or other analysis are performed on epoched data... == 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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