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| * 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. |
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| * '''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. |
* In 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. * '''Extract > Extract time''': 40.00ms - 49.60ms, overwrite initial file * This will extract from each file a small time window around the main response peak. * Selecting the overwrite option will replace the previous file (bandpass), with the output of this process (bandpass+extract). This option is usually unselected for the first process in the list, then selected automatically. * '''Average > Average over time''': Overwrite initial file * Compute the average over this small time window. * '''Export > Export to Matlab variable''': "avg45" * 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. Save your pipeline: Click on the last button in the toolbar > Save > process_avg45. === Saving/exporting a pipeline === The last button in the the toolbar offers a list of menus to save, load and export the pipelines. {{attachment:pipeline3.gif}} * '''Load''': List of processes that are saved in the user preferences * '''Load from file''': Import a pipeline from a pipeline_...mat file (previously saved with the menu "Save as Matlab matrix") * '''Save''': Save the pipeline in the user preferencies, to be able to access it really fast after * '''Save as Matlab matrix''': Exports the pipeline for a Matlab structure in a .mat file. Allows different users to exchange their analysis pipelines (or a single user between different computers). * '''Save as Matlab script''': This option generates a human-readable Matlab script that can be re-used for other purposes or modified. * '''Delete''': Remove a pipeline that is saved in the user preferences. Here is the Matlab script that is generated automatically for this pipeline. . {{attachment:script.gif}} === Running a pipeline === 1. Click on Ok, in the pipeline window. After a few seconds, you will see two new files in the database, and two messages in the Matlab command window. The file names have list of tags that where appended to represent all the processes that were applied to them. <<BR>><<BR>> {{attachment:output.gif}} {{attachment:export.gif}} 1. Quick reminder: the file history record all this information too (right-click > File > View file history), so you are free to rename those files in something shorter (example: "ERF_avg45").<<BR>><<BR>> {{attachment:history.gif}} 1. |
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.
Drag and drop the following nodes in the Process1 list: Right/ERF (recordings), Left (condition), and Subject01 (subject)
- 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]".
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
If you select the third button "Time-frequency", you would see "0" everywhere because there are no time-frequency decompositions in the database yet.
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.
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.
Creating a pipeline
List of processes
Click on Run. The Process selection window 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.
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.
- When you select a process, a list of options specific to this process is shown in the window.
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.
- Now add the following processes, and set their options:
Pre-process > Band-pass filter: 2Hz - 30Hz
- In 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.
Extract > Extract time: 40.00ms - 49.60ms, overwrite initial file
- This will extract from each file a small time window around the main response peak.
- Selecting the overwrite option will replace the previous file (bandpass), with the output of this process (bandpass+extract). This option is usually unselected for the first process in the list, then selected automatically.
Average > Average over time: Overwrite initial file
- Compute the average over this small time window.
Export > Export to Matlab variable: "avg45"
Reads the current file (time window averaged over time) and exports it in a variable in the Matlab workspace.
Save your pipeline: Click on the last button in the toolbar > Save > process_avg45.
Saving/exporting a pipeline
The last button in the the toolbar offers a list of menus to save, load and export the pipelines.
Load: List of processes that are saved in the user preferences
Load from file: Import a pipeline from a pipeline_...mat file (previously saved with the menu "Save as Matlab matrix")
Save: Save the pipeline in the user preferencies, to be able to access it really fast after
Save as Matlab matrix: Exports the pipeline for a Matlab structure in a .mat file. Allows different users to exchange their analysis pipelines (or a single user between different computers).
Save as Matlab script: This option generates a human-readable Matlab script that can be re-used for other purposes or modified.
Delete: Remove a pipeline that is saved in the user preferences.
Here is the Matlab script that is generated automatically for this pipeline.
Running a pipeline
Click on Ok, in the pipeline window. After a few seconds, you will see two new files in the database, and two messages in the Matlab command window. The file names have list of tags that where appended to represent all the processes that were applied to them.
Quick reminder: the file history record all this information too (right-click > File > View file history), so you are free to rename those files in something shorter (example: "ERF_avg45").
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.