= Tutorial 9: Processes =
The main window includes a graphical batching interface that directly benefits from the database explorer: files are organized as a tree of subjects and conditions, and simple drag-and-drop operations readily select files for subsequent batch processing. Most of the Brainstorm features are (or will be) available through this interface, including pre-processing of the recordings, averaging, time-frequency decompositions, and computing statistics. A full analysis pipeline can be created in a few minutes, saved in the user’s preferences and reloaded in one click, executed directly or exported as a Matlab script.

== Selecting files to process ==
First thing to do is to define the files you are going to process. This is done easily by picking files or folders in the database explorer and droping them in the empty list of the Process1 tab.

 1. Drag and drop the following nodes in the Process1 list: Right/ERF (recordings), Left (condition), and Subject01 (subject)<<BR>><<BR>> {{attachment:files1.gif}}
  * A number between brackets appear next to each node: it represents the number of data files that where found in each of them. The node ERF "contains" only itself (1), Subject01/Right contains ERF and Std files (2), and Subject01 contains 2 conditions x 2 recordings (4).
  * The total number of files, ie. the sum of all those values, appears in the title of the panel "Files to process [8]".
 1. The buttons on the left side allow you to select what type of file you want to process: Recordings, sources, time-frequency, other. Now select the second button "Sources". All the counts are updated and now reflect the number of sources files that are found for each node<<BR>><<BR>> {{attachment:files2.gif}}
 1. If you select the third button "Time-frequency", you would see "0" everywhere because there are no time-frequency decompositions in the database yet.<<BR>><<BR>> {{attachment:files3.gif}}
 1. Now clear the list from all the files. You may either right-click on the list (popup menu ''Clear list''), or select all the nodes (holding ''Shift ''or ''Crtl ''key) and then press the ''Delete ''key.
 1. Select both files Left/ERF and Right/ERF in the tree (holding ''Ctrl ''key), and put the in Process list. We are going to apply some functions on those two files. You cannot distiguish them after they are dropped in the list, because they are both referred as "ERP". If at some point you need to know what is in the list, just leave you mouse over a node for a few seconds, and a tooltip would give you information about it. Just like in the database explorer.<<BR>><<BR>> {{attachment:files4.gif}}

== Creating a pipeline ==
 1. Click on Run. The Process selection windows appears, with which you can create an analysis pipeline (ie. a list of process that are applyied on the selected files one after the other). The first button in the toolbar shows the list of processed that are currently available. If you click on a menu, it's added to the list. <<BR>><<BR>> {{attachment:pipeline1.gif}}
 1. Some menus appear in grey (example: Normalize > Spatial smoothing). This means that they are not meant to be applied to the type of data that you have in input, or at the end of the current pipeline. The "spatial smoothing" process may only be run on source files.
 1. When you select a process, a list of options specific to this process is shown in the window.
 1. Now add the following processes, and set their options:
  * '''Pre-process > Band-pass filter''': 2Hz - 30Hz
  * '''Extract > Extract time''': 40.00ms - 49.60ms, overwrite initial file<<BR>>This will extract from each file a small time window around the main response peak. <<BR>>Selecting the overwrite option will replace the previous file (extract time window), with the output of this process. This option is usually unselected for the first process in the list, then selected automatically.
  * '''Average > Average over time''': Overwrite initial file<<BR>>Compute the average over this small time window.
  * '''Export > Export to Matlab variable''': "avg45"<<BR>>Reads the current file (time window averaged over time) and exports it in a variable in the Matlab workspace.<<BR>><<BR>> {{attachment:pipeline2.gif}}
 1. If some processes, you can specify the type(s) of sensors on which you want to apply the process. This way you can for instance apply different filters on the EEG and the MEG, if you have both in the same files.
 1. To delete a process: Select it and press the ''Delete'' key, or the big cross in the toolbar. With the "up arrow" and "down arrow" buttons in the toolbar, you can move up/down a process in the pipeline.

== Available processes ==
== Plugin structure ==
The available processes are organized in a plug-in structure. Any Matlab  script that is added to the plug-in folder and has the right format  will be automatically detected and made available in the GUI. This  mechanism makes the contribution from other developers to Brainstorm  very easy.

=== User processes ===